help regarding gbrowse

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help regarding gbrowse

umay kulsum
I have been trying to install and invoke GBrowse since a month but to
no result....
can someone help me regarding the installation process.

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Re: help regarding gbrowse

Scott Cain
Hi Umay,

Can you please tell us what you done and where you think the process has failed?  For instance, what do you see when you go to the built in sample yeast data set?

Scott

Sent from my iPhone

> On Sep 11, 2014, at 11:41 PM, umay kulsum <[hidden email]> wrote:
>
> I have been trying to install and invoke GBrowse since a month but to
> no result....
> can someone help me regarding the installation process.
>
> ------------------------------------------------------------------------------
> Want excitement?
> Manually upgrade your production database.
> When you want reliability, choose Perforce
> Perforce version control. Predictably reliable.
> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

------------------------------------------------------------------------------
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When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
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Re: help regarding gbrowse

Scott Cain
Umay,

Please "reply-all" so that your replies stay on the GBrowse mailing list.

A few things:

The url you are using is not correct; it should be http://localhost/cgi-bin/gb2/gbrowse/yeast.  This is linked to from http://localhost/gbrowse2/

I don't know why you have two yeast_chr1+2 directories, but only one of them will work.  The typical configuration would be for the one in /var/lib/gbrowse2/databases to work.

The cgi-bin directory is not in the /var/www directory when apache is typically configured for ubuntu; it's in /usr/lib/cgi-bin, as it is in your case.

Scott


On Wed, Sep 17, 2014 at 4:15 AM, umay kulsum <[hidden email]> wrote:
I have installed GBrowse using the command in ubuntu 14.04
sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'

I have the following files:
etc/gbrowse2/GBrowse.conf
var/www/gbrowse2/databases where I have the yeast_chr1+2 folder with
my own data files
usr/lib/cgi-bin/gb2
var/lib/gbrowse2/databases/yeast_chr1+2 with other files

but still the url http://localhost/cgi-bin/gbrowse2/yeast shows the
following url was not found on the server

where is the cgi-bin mentioned in the url located when it is not in /var/www/

On Wed, Sep 17, 2014 at 8:54 AM, umay kulsum <[hidden email]> wrote:
> Hi
> I have installed GBrowse using the command in ubuntu 14.04
> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
> but when I point my browser to
> http://localhost/cgi-bin/gbrowse2/yeast, it shows the following url is
> not found on this server..
> where is the cgi-bin mentioned in the url located when it is not in /var/www/
>
> On Tue, Sep 16, 2014 at 2:28 AM, Scott Cain <[hidden email]> wrote:
>> Hi Umay,
>>
>> Can you please tell us what you done and where you think the process has failed?  For instance, what do you see when you go to the built in sample yeast data set?
>>
>> Scott
>>
>> Sent from my iPhone
>>
>>> On Sep 11, 2014, at 11:41 PM, umay kulsum <[hidden email]> wrote:
>>>
>>> I have been trying to install and invoke GBrowse since a month but to
>>> no result....
>>> can someone help me regarding the installation process.
>>>
>>> ------------------------------------------------------------------------------
>>> Want excitement?
>>> Manually upgrade your production database.
>>> When you want reliability, choose Perforce
>>> Perforce version control. Predictably reliable.
>>> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
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Re: help regarding gbrowse

umay kulsum
hi
I have tried http://localhost/cgi-bin/gb2/gbrowse/yeast also but again
its the same the requested url is not found on the server...
what should I do??
where am I going wrong??
can you please tell me how can I start from scratch that is uninstall
and then reinstall....

On Wed, Sep 17, 2014 at 7:47 PM, Scott Cain <[hidden email]> wrote:

> Umay,
>
> Please "reply-all" so that your replies stay on the GBrowse mailing list.
>
> A few things:
>
> The url you are using is not correct; it should be
> http://localhost/cgi-bin/gb2/gbrowse/yeast.  This is linked to from
> http://localhost/gbrowse2/
>
> I don't know why you have two yeast_chr1+2 directories, but only one of them
> will work.  The typical configuration would be for the one in
> /var/lib/gbrowse2/databases to work.
>
> The cgi-bin directory is not in the /var/www directory when apache is
> typically configured for ubuntu; it's in /usr/lib/cgi-bin, as it is in your
> case.
>
> Scott
>
>
> On Wed, Sep 17, 2014 at 4:15 AM, umay kulsum <[hidden email]> wrote:
>>
>> I have installed GBrowse using the command in ubuntu 14.04
>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>>
>> I have the following files:
>> etc/gbrowse2/GBrowse.conf
>> var/www/gbrowse2/databases where I have the yeast_chr1+2 folder with
>> my own data files
>> usr/lib/cgi-bin/gb2
>> var/lib/gbrowse2/databases/yeast_chr1+2 with other files
>>
>> but still the url http://localhost/cgi-bin/gbrowse2/yeast shows the
>> following url was not found on the server
>>
>> where is the cgi-bin mentioned in the url located when it is not in
>> /var/www/
>>
>> On Wed, Sep 17, 2014 at 8:54 AM, umay kulsum <[hidden email]>
>> wrote:
>> > Hi
>> > I have installed GBrowse using the command in ubuntu 14.04
>> > sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>> > but when I point my browser to
>> > http://localhost/cgi-bin/gbrowse2/yeast, it shows the following url is
>> > not found on this server..
>> > where is the cgi-bin mentioned in the url located when it is not in
>> > /var/www/
>> >
>> > On Tue, Sep 16, 2014 at 2:28 AM, Scott Cain <[hidden email]> wrote:
>> >> Hi Umay,
>> >>
>> >> Can you please tell us what you done and where you think the process
>> >> has failed?  For instance, what do you see when you go to the built in
>> >> sample yeast data set?
>> >>
>> >> Scott
>> >>
>> >> Sent from my iPhone
>> >>
>> >>> On Sep 11, 2014, at 11:41 PM, umay kulsum <[hidden email]>
>> >>> wrote:
>> >>>
>> >>> I have been trying to install and invoke GBrowse since a month but to
>> >>> no result....
>> >>> can someone help me regarding the installation process.
>> >>>
>> >>>
>> >>> ------------------------------------------------------------------------------
>> >>> Want excitement?
>> >>> Manually upgrade your production database.
>> >>> When you want reliability, choose Perforce
>> >>> Perforce version control. Predictably reliable.
>> >>>
>> >>> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
>> >>> _______________________________________________
>> >>> Gmod-gbrowse mailing list
>> >>> [hidden email]
>> >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
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Re: help regarding gbrowse

Scott Cain
Hi Umay,

What does it say in the apache error log?  If you're getting a message about a file not being found, it will record where it was looking for the file. The error log is in /var/log/apache2. The most recent message is at the end of the file.

Scott


Sent from my iPhone

> On Sep 17, 2014, at 11:03 PM, umay kulsum <[hidden email]> wrote:
>
> hi
> I have tried http://localhost/cgi-bin/gb2/gbrowse/yeast also but again
> its the same the requested url is not found on the server...
> what should I do??
> where am I going wrong??
> can you please tell me how can I start from scratch that is uninstall
> and then reinstall....
>
>> On Wed, Sep 17, 2014 at 7:47 PM, Scott Cain <[hidden email]> wrote:
>> Umay,
>>
>> Please "reply-all" so that your replies stay on the GBrowse mailing list.
>>
>> A few things:
>>
>> The url you are using is not correct; it should be
>> http://localhost/cgi-bin/gb2/gbrowse/yeast.  This is linked to from
>> http://localhost/gbrowse2/
>>
>> I don't know why you have two yeast_chr1+2 directories, but only one of them
>> will work.  The typical configuration would be for the one in
>> /var/lib/gbrowse2/databases to work.
>>
>> The cgi-bin directory is not in the /var/www directory when apache is
>> typically configured for ubuntu; it's in /usr/lib/cgi-bin, as it is in your
>> case.
>>
>> Scott
>>
>>
>>> On Wed, Sep 17, 2014 at 4:15 AM, umay kulsum <[hidden email]> wrote:
>>>
>>> I have installed GBrowse using the command in ubuntu 14.04
>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>>>
>>> I have the following files:
>>> etc/gbrowse2/GBrowse.conf
>>> var/www/gbrowse2/databases where I have the yeast_chr1+2 folder with
>>> my own data files
>>> usr/lib/cgi-bin/gb2
>>> var/lib/gbrowse2/databases/yeast_chr1+2 with other files
>>>
>>> but still the url http://localhost/cgi-bin/gbrowse2/yeast shows the
>>> following url was not found on the server
>>>
>>> where is the cgi-bin mentioned in the url located when it is not in
>>> /var/www/
>>>
>>> On Wed, Sep 17, 2014 at 8:54 AM, umay kulsum <[hidden email]>
>>> wrote:
>>>> Hi
>>>> I have installed GBrowse using the command in ubuntu 14.04
>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>>>> but when I point my browser to
>>>> http://localhost/cgi-bin/gbrowse2/yeast, it shows the following url is
>>>> not found on this server..
>>>> where is the cgi-bin mentioned in the url located when it is not in
>>>> /var/www/
>>>>
>>>>> On Tue, Sep 16, 2014 at 2:28 AM, Scott Cain <[hidden email]> wrote:
>>>>> Hi Umay,
>>>>>
>>>>> Can you please tell us what you done and where you think the process
>>>>> has failed?  For instance, what do you see when you go to the built in
>>>>> sample yeast data set?
>>>>>
>>>>> Scott
>>>>>
>>>>> Sent from my iPhone
>>>>>
>>>>>> On Sep 11, 2014, at 11:41 PM, umay kulsum <[hidden email]>
>>>>>> wrote:
>>>>>>
>>>>>> I have been trying to install and invoke GBrowse since a month but to
>>>>>> no result....
>>>>>> can someone help me regarding the installation process.
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> Want excitement?
>>>>>> Manually upgrade your production database.
>>>>>> When you want reliability, choose Perforce
>>>>>> Perforce version control. Predictably reliable.
>>>>>>
>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
>>>>>> _______________________________________________
>>>>>> Gmod-gbrowse mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot
>> net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
_______________________________________________
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Re: help regarding gbrowse

umay kulsum
The apache error log shows :

[Thu Sep 18 09:03:14.584273 2014] [core:notice] [pid 10766] AH00094:
Command line: '/usr/sbin/apache2'


This is the last comment in /var/log/apache2/error.log...... it shows
nothing regarding the files not found


In the access.log file the last comment is :


127.0.0.1 - - [18/Sep/2014:11:13:58 +0530] "GET
/cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513 "-" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:28.0) Gecko/20100101 Firefox/28.0"

On Thu, Sep 18, 2014 at 10:34 AM, Scott Cain <[hidden email]> wrote:

> Hi Umay,
>
> What does it say in the apache error log?  If you're getting a message about a file not being found, it will record where it was looking for the file. The error log is in /var/log/apache2. The most recent message is at the end of the file.
>
> Scott
>
>
> Sent from my iPhone
>
>> On Sep 17, 2014, at 11:03 PM, umay kulsum <[hidden email]> wrote:
>>
>> hi
>> I have tried http://localhost/cgi-bin/gb2/gbrowse/yeast also but again
>> its the same the requested url is not found on the server...
>> what should I do??
>> where am I going wrong??
>> can you please tell me how can I start from scratch that is uninstall
>> and then reinstall....
>>
>>> On Wed, Sep 17, 2014 at 7:47 PM, Scott Cain <[hidden email]> wrote:
>>> Umay,
>>>
>>> Please "reply-all" so that your replies stay on the GBrowse mailing list.
>>>
>>> A few things:
>>>
>>> The url you are using is not correct; it should be
>>> http://localhost/cgi-bin/gb2/gbrowse/yeast.  This is linked to from
>>> http://localhost/gbrowse2/
>>>
>>> I don't know why you have two yeast_chr1+2 directories, but only one of them
>>> will work.  The typical configuration would be for the one in
>>> /var/lib/gbrowse2/databases to work.
>>>
>>> The cgi-bin directory is not in the /var/www directory when apache is
>>> typically configured for ubuntu; it's in /usr/lib/cgi-bin, as it is in your
>>> case.
>>>
>>> Scott
>>>
>>>
>>>> On Wed, Sep 17, 2014 at 4:15 AM, umay kulsum <[hidden email]> wrote:
>>>>
>>>> I have installed GBrowse using the command in ubuntu 14.04
>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>>>>
>>>> I have the following files:
>>>> etc/gbrowse2/GBrowse.conf
>>>> var/www/gbrowse2/databases where I have the yeast_chr1+2 folder with
>>>> my own data files
>>>> usr/lib/cgi-bin/gb2
>>>> var/lib/gbrowse2/databases/yeast_chr1+2 with other files
>>>>
>>>> but still the url http://localhost/cgi-bin/gbrowse2/yeast shows the
>>>> following url was not found on the server
>>>>
>>>> where is the cgi-bin mentioned in the url located when it is not in
>>>> /var/www/
>>>>
>>>> On Wed, Sep 17, 2014 at 8:54 AM, umay kulsum <[hidden email]>
>>>> wrote:
>>>>> Hi
>>>>> I have installed GBrowse using the command in ubuntu 14.04
>>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>>>>> but when I point my browser to
>>>>> http://localhost/cgi-bin/gbrowse2/yeast, it shows the following url is
>>>>> not found on this server..
>>>>> where is the cgi-bin mentioned in the url located when it is not in
>>>>> /var/www/
>>>>>
>>>>>> On Tue, Sep 16, 2014 at 2:28 AM, Scott Cain <[hidden email]> wrote:
>>>>>> Hi Umay,
>>>>>>
>>>>>> Can you please tell us what you done and where you think the process
>>>>>> has failed?  For instance, what do you see when you go to the built in
>>>>>> sample yeast data set?
>>>>>>
>>>>>> Scott
>>>>>>
>>>>>> Sent from my iPhone
>>>>>>
>>>>>>> On Sep 11, 2014, at 11:41 PM, umay kulsum <[hidden email]>
>>>>>>> wrote:
>>>>>>>
>>>>>>> I have been trying to install and invoke GBrowse since a month but to
>>>>>>> no result....
>>>>>>> can someone help me regarding the installation process.
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> Want excitement?
>>>>>>> Manually upgrade your production database.
>>>>>>> When you want reliability, choose Perforce
>>>>>>> Perforce version control. Predictably reliable.
>>>>>>>
>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
>>>>>>> _______________________________________________
>>>>>>> Gmod-gbrowse mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot
>>> net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
_______________________________________________
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Re: help regarding gbrowse

umay kulsum
whenever we write localhost it looks for files in /var/www/html
so I think its looking for /cgi-bin/gb2/gbrowse/yeast in /var/www

On Thu, Sep 18, 2014 at 11:25 AM, umay kulsum <[hidden email]> wrote:

> The apache error log shows :
>
> [Thu Sep 18 09:03:14.584273 2014] [core:notice] [pid 10766] AH00094:
> Command line: '/usr/sbin/apache2'
>
>
> This is the last comment in /var/log/apache2/error.log...... it shows
> nothing regarding the files not found
>
>
> In the access.log file the last comment is :
>
>
> 127.0.0.1 - - [18/Sep/2014:11:13:58 +0530] "GET
> /cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513 "-" "Mozilla/5.0 (X11;
> Ubuntu; Linux x86_64; rv:28.0) Gecko/20100101 Firefox/28.0"
>
> On Thu, Sep 18, 2014 at 10:34 AM, Scott Cain <[hidden email]> wrote:
>> Hi Umay,
>>
>> What does it say in the apache error log?  If you're getting a message about a file not being found, it will record where it was looking for the file. The error log is in /var/log/apache2. The most recent message is at the end of the file.
>>
>> Scott
>>
>>
>> Sent from my iPhone
>>
>>> On Sep 17, 2014, at 11:03 PM, umay kulsum <[hidden email]> wrote:
>>>
>>> hi
>>> I have tried http://localhost/cgi-bin/gb2/gbrowse/yeast also but again
>>> its the same the requested url is not found on the server...
>>> what should I do??
>>> where am I going wrong??
>>> can you please tell me how can I start from scratch that is uninstall
>>> and then reinstall....
>>>
>>>> On Wed, Sep 17, 2014 at 7:47 PM, Scott Cain <[hidden email]> wrote:
>>>> Umay,
>>>>
>>>> Please "reply-all" so that your replies stay on the GBrowse mailing list.
>>>>
>>>> A few things:
>>>>
>>>> The url you are using is not correct; it should be
>>>> http://localhost/cgi-bin/gb2/gbrowse/yeast.  This is linked to from
>>>> http://localhost/gbrowse2/
>>>>
>>>> I don't know why you have two yeast_chr1+2 directories, but only one of them
>>>> will work.  The typical configuration would be for the one in
>>>> /var/lib/gbrowse2/databases to work.
>>>>
>>>> The cgi-bin directory is not in the /var/www directory when apache is
>>>> typically configured for ubuntu; it's in /usr/lib/cgi-bin, as it is in your
>>>> case.
>>>>
>>>> Scott
>>>>
>>>>
>>>>> On Wed, Sep 17, 2014 at 4:15 AM, umay kulsum <[hidden email]> wrote:
>>>>>
>>>>> I have installed GBrowse using the command in ubuntu 14.04
>>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>>>>>
>>>>> I have the following files:
>>>>> etc/gbrowse2/GBrowse.conf
>>>>> var/www/gbrowse2/databases where I have the yeast_chr1+2 folder with
>>>>> my own data files
>>>>> usr/lib/cgi-bin/gb2
>>>>> var/lib/gbrowse2/databases/yeast_chr1+2 with other files
>>>>>
>>>>> but still the url http://localhost/cgi-bin/gbrowse2/yeast shows the
>>>>> following url was not found on the server
>>>>>
>>>>> where is the cgi-bin mentioned in the url located when it is not in
>>>>> /var/www/
>>>>>
>>>>> On Wed, Sep 17, 2014 at 8:54 AM, umay kulsum <[hidden email]>
>>>>> wrote:
>>>>>> Hi
>>>>>> I have installed GBrowse using the command in ubuntu 14.04
>>>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>>>>>> but when I point my browser to
>>>>>> http://localhost/cgi-bin/gbrowse2/yeast, it shows the following url is
>>>>>> not found on this server..
>>>>>> where is the cgi-bin mentioned in the url located when it is not in
>>>>>> /var/www/
>>>>>>
>>>>>>> On Tue, Sep 16, 2014 at 2:28 AM, Scott Cain <[hidden email]> wrote:
>>>>>>> Hi Umay,
>>>>>>>
>>>>>>> Can you please tell us what you done and where you think the process
>>>>>>> has failed?  For instance, what do you see when you go to the built in
>>>>>>> sample yeast data set?
>>>>>>>
>>>>>>> Scott
>>>>>>>
>>>>>>> Sent from my iPhone
>>>>>>>
>>>>>>>> On Sep 11, 2014, at 11:41 PM, umay kulsum <[hidden email]>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>> I have been trying to install and invoke GBrowse since a month but to
>>>>>>>> no result....
>>>>>>>> can someone help me regarding the installation process.
>>>>>>>>
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> Want excitement?
>>>>>>>> Manually upgrade your production database.
>>>>>>>> When you want reliability, choose Perforce
>>>>>>>> Perforce version control. Predictably reliable.
>>>>>>>>
>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
>>>>>>>> _______________________________________________
>>>>>>>> Gmod-gbrowse mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain dot
>>>> net
>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
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Re: help regarding gbrowse

Scott Cain
Hi Umay,

I suspect you are using Ubuntu 14.04 (you may have already told me that--I don't remember).  While working recently on some minor bug fixes for GBrowse, we discovered that when Ubuntu 14.04 was released, they dramatically rearranged the file structure for system files, which broke the GBrowse installer.  The easiest way to install GBrowse correctly at the moment is to get a GitHub checkout of the current source and install that way.  It's fairly straight forward; this is what you do:

git clone https://github.com/GMOD/GBrowse.git
cd GBrowse
perl Build.PL  #accepting the defaults should be fine
./Build
./Build test
sudo ./Build install

After doing that you should be able to go to http://localhost/gbrowse2 though the links for sample data sets are written assuming you have fastcgi installed (which is a good idea to use, because it makes things faster), but if you don't have fastcgi, you should still be able to go to http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset.  If that works, you should be able to proceed with the tutorial as well.

On Thu, Sep 18, 2014 at 2:15 AM, umay kulsum <[hidden email]> wrote:
whenever we write localhost it looks for files in /var/www/html
so I think its looking for /cgi-bin/gb2/gbrowse/yeast in /var/www

On Thu, Sep 18, 2014 at 11:25 AM, umay kulsum <[hidden email]> wrote:
> The apache error log shows :
>
> [Thu Sep 18 09:03:14.584273 2014] [core:notice] [pid 10766] AH00094:
> Command line: '/usr/sbin/apache2'
>
>
> This is the last comment in /var/log/apache2/error.log...... it shows
> nothing regarding the files not found
>
>
> In the access.log file the last comment is :
>
>
> 127.0.0.1 - - [18/Sep/2014:11:13:58 +0530] "GET
> /cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513 "-" "Mozilla/5.0 (X11;
> Ubuntu; Linux x86_64; rv:28.0) Gecko/20100101 Firefox/28.0"
>
> On Thu, Sep 18, 2014 at 10:34 AM, Scott Cain <[hidden email]> wrote:
>> Hi Umay,
>>
>> What does it say in the apache error log?  If you're getting a message about a file not being found, it will record where it was looking for the file. The error log is in /var/log/apache2. The most recent message is at the end of the file.
>>
>> Scott
>>
>>
>> Sent from my iPhone
>>
>>> On Sep 17, 2014, at 11:03 PM, umay kulsum <[hidden email]> wrote:
>>>
>>> hi
>>> I have tried http://localhost/cgi-bin/gb2/gbrowse/yeast also but again
>>> its the same the requested url is not found on the server...
>>> what should I do??
>>> where am I going wrong??
>>> can you please tell me how can I start from scratch that is uninstall
>>> and then reinstall....
>>>
>>>> On Wed, Sep 17, 2014 at 7:47 PM, Scott Cain <[hidden email]> wrote:
>>>> Umay,
>>>>
>>>> Please "reply-all" so that your replies stay on the GBrowse mailing list.
>>>>
>>>> A few things:
>>>>
>>>> The url you are using is not correct; it should be
>>>> http://localhost/cgi-bin/gb2/gbrowse/yeast.  This is linked to from
>>>> http://localhost/gbrowse2/
>>>>
>>>> I don't know why you have two yeast_chr1+2 directories, but only one of them
>>>> will work.  The typical configuration would be for the one in
>>>> /var/lib/gbrowse2/databases to work.
>>>>
>>>> The cgi-bin directory is not in the /var/www directory when apache is
>>>> typically configured for ubuntu; it's in /usr/lib/cgi-bin, as it is in your
>>>> case.
>>>>
>>>> Scott
>>>>
>>>>
>>>>> On Wed, Sep 17, 2014 at 4:15 AM, umay kulsum <[hidden email]> wrote:
>>>>>
>>>>> I have installed GBrowse using the command in ubuntu 14.04
>>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>>>>>
>>>>> I have the following files:
>>>>> etc/gbrowse2/GBrowse.conf
>>>>> var/www/gbrowse2/databases where I have the yeast_chr1+2 folder with
>>>>> my own data files
>>>>> usr/lib/cgi-bin/gb2
>>>>> var/lib/gbrowse2/databases/yeast_chr1+2 with other files
>>>>>
>>>>> but still the url http://localhost/cgi-bin/gbrowse2/yeast shows the
>>>>> following url was not found on the server
>>>>>
>>>>> where is the cgi-bin mentioned in the url located when it is not in
>>>>> /var/www/
>>>>>
>>>>> On Wed, Sep 17, 2014 at 8:54 AM, umay kulsum <[hidden email]>
>>>>> wrote:
>>>>>> Hi
>>>>>> I have installed GBrowse using the command in ubuntu 14.04
>>>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>>>>>> but when I point my browser to
>>>>>> http://localhost/cgi-bin/gbrowse2/yeast, it shows the following url is
>>>>>> not found on this server..
>>>>>> where is the cgi-bin mentioned in the url located when it is not in
>>>>>> /var/www/
>>>>>>
>>>>>>> On Tue, Sep 16, 2014 at 2:28 AM, Scott Cain <[hidden email]> wrote:
>>>>>>> Hi Umay,
>>>>>>>
>>>>>>> Can you please tell us what you done and where you think the process
>>>>>>> has failed?  For instance, what do you see when you go to the built in
>>>>>>> sample yeast data set?
>>>>>>>
>>>>>>> Scott
>>>>>>>
>>>>>>> Sent from my iPhone
>>>>>>>
>>>>>>>> On Sep 11, 2014, at 11:41 PM, umay kulsum <[hidden email]>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>> I have been trying to install and invoke GBrowse since a month but to
>>>>>>>> no result....
>>>>>>>> can someone help me regarding the installation process.
>>>>>>>>
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> Want excitement?
>>>>>>>> Manually upgrade your production database.
>>>>>>>> When you want reliability, choose Perforce
>>>>>>>> Perforce version control. Predictably reliable.
>>>>>>>>
>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
>>>>>>>> _______________________________________________
>>>>>>>> Gmod-gbrowse mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain dot
>>>> net
>>>> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
>>>> Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
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Re: help regarding gbrowse

umay kulsum
Hi

when I do
git clone https://github.com/GMOD/GBrowse.git

I get the following error:

Cloning into 'GBrowse'...
fatal: unable to access 'https://github.com/GMOD/GBrowse.git/':
gnutls_handshake() failed: A TLS packet with unexpected length was
received.

On Thu, Sep 18, 2014 at 7:37 PM, Scott Cain <[hidden email]> wrote:

> Hi Umay,
>
> I suspect you are using Ubuntu 14.04 (you may have already told me that--I
> don't remember).  While working recently on some minor bug fixes for
> GBrowse, we discovered that when Ubuntu 14.04 was released, they
> dramatically rearranged the file structure for system files, which broke the
> GBrowse installer.  The easiest way to install GBrowse correctly at the
> moment is to get a GitHub checkout of the current source and install that
> way.  It's fairly straight forward; this is what you do:
>
> git clone https://github.com/GMOD/GBrowse.git
> cd GBrowse
> perl Build.PL  #accepting the defaults should be fine
> ./Build
> ./Build test
> sudo ./Build install
>
> After doing that you should be able to go to http://localhost/gbrowse2
> though the links for sample data sets are written assuming you have fastcgi
> installed (which is a good idea to use, because it makes things faster), but
> if you don't have fastcgi, you should still be able to go to
> http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset.  If that
> works, you should be able to proceed with the tutorial as well.
>
> On Thu, Sep 18, 2014 at 2:15 AM, umay kulsum <[hidden email]> wrote:
>>
>> whenever we write localhost it looks for files in /var/www/html
>> so I think its looking for /cgi-bin/gb2/gbrowse/yeast in /var/www
>>
>> On Thu, Sep 18, 2014 at 11:25 AM, umay kulsum <[hidden email]>
>> wrote:
>> > The apache error log shows :
>> >
>> > [Thu Sep 18 09:03:14.584273 2014] [core:notice] [pid 10766] AH00094:
>> > Command line: '/usr/sbin/apache2'
>> >
>> >
>> > This is the last comment in /var/log/apache2/error.log...... it shows
>> > nothing regarding the files not found
>> >
>> >
>> > In the access.log file the last comment is :
>> >
>> >
>> > 127.0.0.1 - - [18/Sep/2014:11:13:58 +0530] "GET
>> > /cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513 "-" "Mozilla/5.0 (X11;
>> > Ubuntu; Linux x86_64; rv:28.0) Gecko/20100101 Firefox/28.0"
>> >
>> > On Thu, Sep 18, 2014 at 10:34 AM, Scott Cain <[hidden email]>
>> > wrote:
>> >> Hi Umay,
>> >>
>> >> What does it say in the apache error log?  If you're getting a message
>> >> about a file not being found, it will record where it was looking for the
>> >> file. The error log is in /var/log/apache2. The most recent message is at
>> >> the end of the file.
>> >>
>> >> Scott
>> >>
>> >>
>> >> Sent from my iPhone
>> >>
>> >>> On Sep 17, 2014, at 11:03 PM, umay kulsum <[hidden email]>
>> >>> wrote:
>> >>>
>> >>> hi
>> >>> I have tried http://localhost/cgi-bin/gb2/gbrowse/yeast also but again
>> >>> its the same the requested url is not found on the server...
>> >>> what should I do??
>> >>> where am I going wrong??
>> >>> can you please tell me how can I start from scratch that is uninstall
>> >>> and then reinstall....
>> >>>
>> >>>> On Wed, Sep 17, 2014 at 7:47 PM, Scott Cain <[hidden email]>
>> >>>> wrote:
>> >>>> Umay,
>> >>>>
>> >>>> Please "reply-all" so that your replies stay on the GBrowse mailing
>> >>>> list.
>> >>>>
>> >>>> A few things:
>> >>>>
>> >>>> The url you are using is not correct; it should be
>> >>>> http://localhost/cgi-bin/gb2/gbrowse/yeast.  This is linked to from
>> >>>> http://localhost/gbrowse2/
>> >>>>
>> >>>> I don't know why you have two yeast_chr1+2 directories, but only one
>> >>>> of them
>> >>>> will work.  The typical configuration would be for the one in
>> >>>> /var/lib/gbrowse2/databases to work.
>> >>>>
>> >>>> The cgi-bin directory is not in the /var/www directory when apache is
>> >>>> typically configured for ubuntu; it's in /usr/lib/cgi-bin, as it is
>> >>>> in your
>> >>>> case.
>> >>>>
>> >>>> Scott
>> >>>>
>> >>>>
>> >>>>> On Wed, Sep 17, 2014 at 4:15 AM, umay kulsum <[hidden email]>
>> >>>>> wrote:
>> >>>>>
>> >>>>> I have installed GBrowse using the command in ubuntu 14.04
>> >>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>> >>>>>
>> >>>>> I have the following files:
>> >>>>> etc/gbrowse2/GBrowse.conf
>> >>>>> var/www/gbrowse2/databases where I have the yeast_chr1+2 folder with
>> >>>>> my own data files
>> >>>>> usr/lib/cgi-bin/gb2
>> >>>>> var/lib/gbrowse2/databases/yeast_chr1+2 with other files
>> >>>>>
>> >>>>> but still the url http://localhost/cgi-bin/gbrowse2/yeast shows the
>> >>>>> following url was not found on the server
>> >>>>>
>> >>>>> where is the cgi-bin mentioned in the url located when it is not in
>> >>>>> /var/www/
>> >>>>>
>> >>>>> On Wed, Sep 17, 2014 at 8:54 AM, umay kulsum <[hidden email]>
>> >>>>> wrote:
>> >>>>>> Hi
>> >>>>>> I have installed GBrowse using the command in ubuntu 14.04
>> >>>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>> >>>>>> but when I point my browser to
>> >>>>>> http://localhost/cgi-bin/gbrowse2/yeast, it shows the following url
>> >>>>>> is
>> >>>>>> not found on this server..
>> >>>>>> where is the cgi-bin mentioned in the url located when it is not in
>> >>>>>> /var/www/
>> >>>>>>
>> >>>>>>> On Tue, Sep 16, 2014 at 2:28 AM, Scott Cain <[hidden email]>
>> >>>>>>> wrote:
>> >>>>>>> Hi Umay,
>> >>>>>>>
>> >>>>>>> Can you please tell us what you done and where you think the
>> >>>>>>> process
>> >>>>>>> has failed?  For instance, what do you see when you go to the
>> >>>>>>> built in
>> >>>>>>> sample yeast data set?
>> >>>>>>>
>> >>>>>>> Scott
>> >>>>>>>
>> >>>>>>> Sent from my iPhone
>> >>>>>>>
>> >>>>>>>> On Sep 11, 2014, at 11:41 PM, umay kulsum <[hidden email]>
>> >>>>>>>> wrote:
>> >>>>>>>>
>> >>>>>>>> I have been trying to install and invoke GBrowse since a month
>> >>>>>>>> but to
>> >>>>>>>> no result....
>> >>>>>>>> can someone help me regarding the installation process.
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>> ------------------------------------------------------------------------------
>> >>>>>>>> Want excitement?
>> >>>>>>>> Manually upgrade your production database.
>> >>>>>>>> When you want reliability, choose Perforce
>> >>>>>>>> Perforce version control. Predictably reliable.
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
>> >>>>>>>> _______________________________________________
>> >>>>>>>> Gmod-gbrowse mailing list
>> >>>>>>>> [hidden email]
>> >>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>> --
>> >>>>
>> >>>> ------------------------------------------------------------------------
>> >>>> Scott Cain, Ph. D.                                   scott at
>> >>>> scottcain dot
>> >>>> net
>> >>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >>>> Ontario Institute for Cancer Research
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research

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Re: help regarding gbrowse

Scott Cain
Hi Umay,

I don't really know what the problem is--my guess is that there is a network problem.  Can you try from a different network?  Can you clone other things from git but just not GBrowse (I would find that pretty strange if it were the case)?  Also, in case there is a problem with any of the software packages you are using, you should probably run

  sudo apt-get update 
  sudo apt-get upgrade

to make sure your system is up to date.

Scott


On Mon, Sep 22, 2014 at 4:17 AM, umay kulsum <[hidden email]> wrote:
Hi

when I do
git clone https://github.com/GMOD/GBrowse.git

I get the following error:

Cloning into 'GBrowse'...
fatal: unable to access 'https://github.com/GMOD/GBrowse.git/':
gnutls_handshake() failed: A TLS packet with unexpected length was
received.

On Thu, Sep 18, 2014 at 7:37 PM, Scott Cain <[hidden email]> wrote:
> Hi Umay,
>
> I suspect you are using Ubuntu 14.04 (you may have already told me that--I
> don't remember).  While working recently on some minor bug fixes for
> GBrowse, we discovered that when Ubuntu 14.04 was released, they
> dramatically rearranged the file structure for system files, which broke the
> GBrowse installer.  The easiest way to install GBrowse correctly at the
> moment is to get a GitHub checkout of the current source and install that
> way.  It's fairly straight forward; this is what you do:
>
> git clone https://github.com/GMOD/GBrowse.git
> cd GBrowse
> perl Build.PL  #accepting the defaults should be fine
> ./Build
> ./Build test
> sudo ./Build install
>
> After doing that you should be able to go to http://localhost/gbrowse2
> though the links for sample data sets are written assuming you have fastcgi
> installed (which is a good idea to use, because it makes things faster), but
> if you don't have fastcgi, you should still be able to go to
> http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset.  If that
> works, you should be able to proceed with the tutorial as well.
>
> On Thu, Sep 18, 2014 at 2:15 AM, umay kulsum <[hidden email]> wrote:
>>
>> whenever we write localhost it looks for files in /var/www/html
>> so I think its looking for /cgi-bin/gb2/gbrowse/yeast in /var/www
>>
>> On Thu, Sep 18, 2014 at 11:25 AM, umay kulsum <[hidden email]>
>> wrote:
>> > The apache error log shows :
>> >
>> > [Thu Sep 18 09:03:14.584273 2014] [core:notice] [pid 10766] AH00094:
>> > Command line: '/usr/sbin/apache2'
>> >
>> >
>> > This is the last comment in /var/log/apache2/error.log...... it shows
>> > nothing regarding the files not found
>> >
>> >
>> > In the access.log file the last comment is :
>> >
>> >
>> > 127.0.0.1 - - [18/Sep/2014:11:13:58 +0530] "GET
>> > /cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513 "-" "Mozilla/5.0 (X11;
>> > Ubuntu; Linux x86_64; rv:28.0) Gecko/20100101 Firefox/28.0"
>> >
>> > On Thu, Sep 18, 2014 at 10:34 AM, Scott Cain <[hidden email]>
>> > wrote:
>> >> Hi Umay,
>> >>
>> >> What does it say in the apache error log?  If you're getting a message
>> >> about a file not being found, it will record where it was looking for the
>> >> file. The error log is in /var/log/apache2. The most recent message is at
>> >> the end of the file.
>> >>
>> >> Scott
>> >>
>> >>
>> >> Sent from my iPhone
>> >>
>> >>> On Sep 17, 2014, at 11:03 PM, umay kulsum <[hidden email]>
>> >>> wrote:
>> >>>
>> >>> hi
>> >>> I have tried http://localhost/cgi-bin/gb2/gbrowse/yeast also but again
>> >>> its the same the requested url is not found on the server...
>> >>> what should I do??
>> >>> where am I going wrong??
>> >>> can you please tell me how can I start from scratch that is uninstall
>> >>> and then reinstall....
>> >>>
>> >>>> On Wed, Sep 17, 2014 at 7:47 PM, Scott Cain <[hidden email]>
>> >>>> wrote:
>> >>>> Umay,
>> >>>>
>> >>>> Please "reply-all" so that your replies stay on the GBrowse mailing
>> >>>> list.
>> >>>>
>> >>>> A few things:
>> >>>>
>> >>>> The url you are using is not correct; it should be
>> >>>> http://localhost/cgi-bin/gb2/gbrowse/yeast.  This is linked to from
>> >>>> http://localhost/gbrowse2/
>> >>>>
>> >>>> I don't know why you have two yeast_chr1+2 directories, but only one
>> >>>> of them
>> >>>> will work.  The typical configuration would be for the one in
>> >>>> /var/lib/gbrowse2/databases to work.
>> >>>>
>> >>>> The cgi-bin directory is not in the /var/www directory when apache is
>> >>>> typically configured for ubuntu; it's in /usr/lib/cgi-bin, as it is
>> >>>> in your
>> >>>> case.
>> >>>>
>> >>>> Scott
>> >>>>
>> >>>>
>> >>>>> On Wed, Sep 17, 2014 at 4:15 AM, umay kulsum <[hidden email]>
>> >>>>> wrote:
>> >>>>>
>> >>>>> I have installed GBrowse using the command in ubuntu 14.04
>> >>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>> >>>>>
>> >>>>> I have the following files:
>> >>>>> etc/gbrowse2/GBrowse.conf
>> >>>>> var/www/gbrowse2/databases where I have the yeast_chr1+2 folder with
>> >>>>> my own data files
>> >>>>> usr/lib/cgi-bin/gb2
>> >>>>> var/lib/gbrowse2/databases/yeast_chr1+2 with other files
>> >>>>>
>> >>>>> but still the url http://localhost/cgi-bin/gbrowse2/yeast shows the
>> >>>>> following url was not found on the server
>> >>>>>
>> >>>>> where is the cgi-bin mentioned in the url located when it is not in
>> >>>>> /var/www/
>> >>>>>
>> >>>>> On Wed, Sep 17, 2014 at 8:54 AM, umay kulsum <[hidden email]>
>> >>>>> wrote:
>> >>>>>> Hi
>> >>>>>> I have installed GBrowse using the command in ubuntu 14.04
>> >>>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>> >>>>>> but when I point my browser to
>> >>>>>> http://localhost/cgi-bin/gbrowse2/yeast, it shows the following url
>> >>>>>> is
>> >>>>>> not found on this server..
>> >>>>>> where is the cgi-bin mentioned in the url located when it is not in
>> >>>>>> /var/www/
>> >>>>>>
>> >>>>>>> On Tue, Sep 16, 2014 at 2:28 AM, Scott Cain <[hidden email]>
>> >>>>>>> wrote:
>> >>>>>>> Hi Umay,
>> >>>>>>>
>> >>>>>>> Can you please tell us what you done and where you think the
>> >>>>>>> process
>> >>>>>>> has failed?  For instance, what do you see when you go to the
>> >>>>>>> built in
>> >>>>>>> sample yeast data set?
>> >>>>>>>
>> >>>>>>> Scott
>> >>>>>>>
>> >>>>>>> Sent from my iPhone
>> >>>>>>>
>> >>>>>>>> On Sep 11, 2014, at 11:41 PM, umay kulsum <[hidden email]>
>> >>>>>>>> wrote:
>> >>>>>>>>
>> >>>>>>>> I have been trying to install and invoke GBrowse since a month
>> >>>>>>>> but to
>> >>>>>>>> no result....
>> >>>>>>>> can someone help me regarding the installation process.
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>> ------------------------------------------------------------------------------
>> >>>>>>>> Want excitement?
>> >>>>>>>> Manually upgrade your production database.
>> >>>>>>>> When you want reliability, choose Perforce
>> >>>>>>>> Perforce version control. Predictably reliable.
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
>> >>>>>>>> _______________________________________________
>> >>>>>>>> Gmod-gbrowse mailing list
>> >>>>>>>> [hidden email]
>> >>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>> --
>> >>>>
>> >>>> ------------------------------------------------------------------------
>> >>>> Scott Cain, Ph. D.                                   scott at
>> >>>> scottcain dot
>> >>>> net
>> >>>> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
>> >>>> Ontario Institute for Cancer Research
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
> Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
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Re: help regarding gbrowse

umay kulsum
Hi

Thank you scott....got GBrowse installed with git clone...
example database of yeast is also working properly...

but now I have created my own conf file as 114635370.conf in
etc/gbrowse2/gbrowse.conf folder but when I run
http://localhost/cgi-bin/gb2/gbrowse/114635370 it gives the result of
yeast but not my own file
why is it so and what can I do for that??


my conf file is as follows:

[GENERAL]
description   = motifs of 114635370protein
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
               -dir    '/var/www/html/gbrowse2/databases/1/1/4/114635370/'


plugins = BatchDumper FastaDumper
gbrowse root = gbrowse
stylesheet   = gbrowse.css
buttons      = images/buttons
js           = js
tmpimages    = tmp
region segment = 500
initial landmark = 114635370
balloon tips    = 1
drag and drop = 1
cache time    = 1
link          = AUTO
image widths  = 450 640 800 1024
hilite fill    = beige
hilite outline = red
default width = 800
default features = 114635370
max segment     = 500
default segment = 50
zoom levels    = 50 100 200 1000 2000 5000 10000 20000 40000 100000
200000 500000 1000000
show sources   = 1
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
key bgcolor      = beige
examples = 114635370
automatic classes = 114635370


[protein]
feature      = protein
glyph        = so_transcript
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise
height       = 6
description  = 1
balloon hover width = 350
balloon hover = sub { my  = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
     <tr><th rowspan="5" align="left"><br>
     This protein brought to you by <a
href="http://www.expasy.ch">EXPASY</a>.</th>
         <th bgcolor="cyan">Gene </th>
     </tr>
      <tr align='left'><th><a
href="/cgi-bin/gbrowse_details/motif?name=">See protein
details</a></th></tr>
     <tr align='left'><th><a
href="http://www.ncbi.nlm.nih.gov/protein/114635370">Go to
NCBI</a></th></tr>
      </table>

key          = protein
[pattern]
feature      = pattern
glyph        = so_transcript
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise
height       = 6
description  = 1
balloon hover width = 350
balloon hover = sub { my  = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
      <tr><th rowspan="5" align="left"><br>
      This protein brought to you by <a
href="http://www.expasy.ch">EXPASY</a>.</th>
         <th bgcolor="cyan">Gene </th>
      </tr>
      <tr align='left'><th><a
href="/cgi-bin/gbrowse_details/motif?name=">See gene
details</a></th></tr>
     <tr align='left'><th><a
href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
Wikipedia about </a></th></tr>
      <tr align='left'><th><a
href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
      </table>

key           = pattern



[profile]
feature      = profile
glyph        = so_transcript
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise
height       = 6
description  = 0
balloon hover width = 350
balloon hover = sub { my  = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
      <tr><th rowspan="5" align="left"><br>
      This protein brought to you by <a
href="http://www.expasy.ch">EXPASY</a>.</th>
          <th bgcolor="cyan">Gene </th>
     </tr>
      <tr align='left'><th><a
href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
Wikipedia about </a></th></tr>
     <tr align='left'><th><a
href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
     </table>
key          = profile

On Mon, Sep 22, 2014 at 5:36 PM, Scott Cain <[hidden email]> wrote:

> Hi Umay,
>
> I don't really know what the problem is--my guess is that there is a network
> problem.  Can you try from a different network?  Can you clone other things
> from git but just not GBrowse (I would find that pretty strange if it were
> the case)?  Also, in case there is a problem with any of the software
> packages you are using, you should probably run
>
>   sudo apt-get update
>   sudo apt-get upgrade
>
> to make sure your system is up to date.
>
> Scott
>
>
> On Mon, Sep 22, 2014 at 4:17 AM, umay kulsum <[hidden email]> wrote:
>>
>> Hi
>>
>> when I do
>> git clone https://github.com/GMOD/GBrowse.git
>>
>> I get the following error:
>>
>> Cloning into 'GBrowse'...
>> fatal: unable to access 'https://github.com/GMOD/GBrowse.git/':
>> gnutls_handshake() failed: A TLS packet with unexpected length was
>> received.
>>
>> On Thu, Sep 18, 2014 at 7:37 PM, Scott Cain <[hidden email]> wrote:
>> > Hi Umay,
>> >
>> > I suspect you are using Ubuntu 14.04 (you may have already told me
>> > that--I
>> > don't remember).  While working recently on some minor bug fixes for
>> > GBrowse, we discovered that when Ubuntu 14.04 was released, they
>> > dramatically rearranged the file structure for system files, which broke
>> > the
>> > GBrowse installer.  The easiest way to install GBrowse correctly at the
>> > moment is to get a GitHub checkout of the current source and install
>> > that
>> > way.  It's fairly straight forward; this is what you do:
>> >
>> > git clone https://github.com/GMOD/GBrowse.git
>> > cd GBrowse
>> > perl Build.PL  #accepting the defaults should be fine
>> > ./Build
>> > ./Build test
>> > sudo ./Build install
>> >
>> > After doing that you should be able to go to http://localhost/gbrowse2
>> > though the links for sample data sets are written assuming you have
>> > fastcgi
>> > installed (which is a good idea to use, because it makes things faster),
>> > but
>> > if you don't have fastcgi, you should still be able to go to
>> > http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset.  If
>> > that
>> > works, you should be able to proceed with the tutorial as well.
>> >
>> > On Thu, Sep 18, 2014 at 2:15 AM, umay kulsum <[hidden email]>
>> > wrote:
>> >>
>> >> whenever we write localhost it looks for files in /var/www/html
>> >> so I think its looking for /cgi-bin/gb2/gbrowse/yeast in /var/www
>> >>
>> >> On Thu, Sep 18, 2014 at 11:25 AM, umay kulsum <[hidden email]>
>> >> wrote:
>> >> > The apache error log shows :
>> >> >
>> >> > [Thu Sep 18 09:03:14.584273 2014] [core:notice] [pid 10766] AH00094:
>> >> > Command line: '/usr/sbin/apache2'
>> >> >
>> >> >
>> >> > This is the last comment in /var/log/apache2/error.log...... it shows
>> >> > nothing regarding the files not found
>> >> >
>> >> >
>> >> > In the access.log file the last comment is :
>> >> >
>> >> >
>> >> > 127.0.0.1 - - [18/Sep/2014:11:13:58 +0530] "GET
>> >> > /cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513 "-" "Mozilla/5.0 (X11;
>> >> > Ubuntu; Linux x86_64; rv:28.0) Gecko/20100101 Firefox/28.0"
>> >> >
>> >> > On Thu, Sep 18, 2014 at 10:34 AM, Scott Cain <[hidden email]>
>> >> > wrote:
>> >> >> Hi Umay,
>> >> >>
>> >> >> What does it say in the apache error log?  If you're getting a
>> >> >> message
>> >> >> about a file not being found, it will record where it was looking
>> >> >> for the
>> >> >> file. The error log is in /var/log/apache2. The most recent message
>> >> >> is at
>> >> >> the end of the file.
>> >> >>
>> >> >> Scott
>> >> >>
>> >> >>
>> >> >> Sent from my iPhone
>> >> >>
>> >> >>> On Sep 17, 2014, at 11:03 PM, umay kulsum <[hidden email]>
>> >> >>> wrote:
>> >> >>>
>> >> >>> hi
>> >> >>> I have tried http://localhost/cgi-bin/gb2/gbrowse/yeast also but
>> >> >>> again
>> >> >>> its the same the requested url is not found on the server...
>> >> >>> what should I do??
>> >> >>> where am I going wrong??
>> >> >>> can you please tell me how can I start from scratch that is
>> >> >>> uninstall
>> >> >>> and then reinstall....
>> >> >>>
>> >> >>>> On Wed, Sep 17, 2014 at 7:47 PM, Scott Cain <[hidden email]>
>> >> >>>> wrote:
>> >> >>>> Umay,
>> >> >>>>
>> >> >>>> Please "reply-all" so that your replies stay on the GBrowse
>> >> >>>> mailing
>> >> >>>> list.
>> >> >>>>
>> >> >>>> A few things:
>> >> >>>>
>> >> >>>> The url you are using is not correct; it should be
>> >> >>>> http://localhost/cgi-bin/gb2/gbrowse/yeast.  This is linked to
>> >> >>>> from
>> >> >>>> http://localhost/gbrowse2/
>> >> >>>>
>> >> >>>> I don't know why you have two yeast_chr1+2 directories, but only
>> >> >>>> one
>> >> >>>> of them
>> >> >>>> will work.  The typical configuration would be for the one in
>> >> >>>> /var/lib/gbrowse2/databases to work.
>> >> >>>>
>> >> >>>> The cgi-bin directory is not in the /var/www directory when apache
>> >> >>>> is
>> >> >>>> typically configured for ubuntu; it's in /usr/lib/cgi-bin, as it
>> >> >>>> is
>> >> >>>> in your
>> >> >>>> case.
>> >> >>>>
>> >> >>>> Scott
>> >> >>>>
>> >> >>>>
>> >> >>>>> On Wed, Sep 17, 2014 at 4:15 AM, umay kulsum
>> >> >>>>> <[hidden email]>
>> >> >>>>> wrote:
>> >> >>>>>
>> >> >>>>> I have installed GBrowse using the command in ubuntu 14.04
>> >> >>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>> >> >>>>>
>> >> >>>>> I have the following files:
>> >> >>>>> etc/gbrowse2/GBrowse.conf
>> >> >>>>> var/www/gbrowse2/databases where I have the yeast_chr1+2 folder
>> >> >>>>> with
>> >> >>>>> my own data files
>> >> >>>>> usr/lib/cgi-bin/gb2
>> >> >>>>> var/lib/gbrowse2/databases/yeast_chr1+2 with other files
>> >> >>>>>
>> >> >>>>> but still the url http://localhost/cgi-bin/gbrowse2/yeast shows
>> >> >>>>> the
>> >> >>>>> following url was not found on the server
>> >> >>>>>
>> >> >>>>> where is the cgi-bin mentioned in the url located when it is not
>> >> >>>>> in
>> >> >>>>> /var/www/
>> >> >>>>>
>> >> >>>>> On Wed, Sep 17, 2014 at 8:54 AM, umay kulsum
>> >> >>>>> <[hidden email]>
>> >> >>>>> wrote:
>> >> >>>>>> Hi
>> >> >>>>>> I have installed GBrowse using the command in ubuntu 14.04
>> >> >>>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>> >> >>>>>> but when I point my browser to
>> >> >>>>>> http://localhost/cgi-bin/gbrowse2/yeast, it shows the following
>> >> >>>>>> url
>> >> >>>>>> is
>> >> >>>>>> not found on this server..
>> >> >>>>>> where is the cgi-bin mentioned in the url located when it is not
>> >> >>>>>> in
>> >> >>>>>> /var/www/
>> >> >>>>>>
>> >> >>>>>>> On Tue, Sep 16, 2014 at 2:28 AM, Scott Cain
>> >> >>>>>>> <[hidden email]>
>> >> >>>>>>> wrote:
>> >> >>>>>>> Hi Umay,
>> >> >>>>>>>
>> >> >>>>>>> Can you please tell us what you done and where you think the
>> >> >>>>>>> process
>> >> >>>>>>> has failed?  For instance, what do you see when you go to the
>> >> >>>>>>> built in
>> >> >>>>>>> sample yeast data set?
>> >> >>>>>>>
>> >> >>>>>>> Scott
>> >> >>>>>>>
>> >> >>>>>>> Sent from my iPhone
>> >> >>>>>>>
>> >> >>>>>>>> On Sep 11, 2014, at 11:41 PM, umay kulsum
>> >> >>>>>>>> <[hidden email]>
>> >> >>>>>>>> wrote:
>> >> >>>>>>>>
>> >> >>>>>>>> I have been trying to install and invoke GBrowse since a month
>> >> >>>>>>>> but to
>> >> >>>>>>>> no result....
>> >> >>>>>>>> can someone help me regarding the installation process.
>> >> >>>>>>>>
>> >> >>>>>>>>
>> >> >>>>>>>>
>> >> >>>>>>>>
>> >> >>>>>>>> ------------------------------------------------------------------------------
>> >> >>>>>>>> Want excitement?
>> >> >>>>>>>> Manually upgrade your production database.
>> >> >>>>>>>> When you want reliability, choose Perforce
>> >> >>>>>>>> Perforce version control. Predictably reliable.
>> >> >>>>>>>>
>> >> >>>>>>>>
>> >> >>>>>>>>
>> >> >>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
>> >> >>>>>>>> _______________________________________________
>> >> >>>>>>>> Gmod-gbrowse mailing list
>> >> >>>>>>>> [hidden email]
>> >> >>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >> >>>>
>> >> >>>>
>> >> >>>>
>> >> >>>>
>> >> >>>> --
>> >> >>>>
>> >> >>>>
>> >> >>>> ------------------------------------------------------------------------
>> >> >>>> Scott Cain, Ph. D.                                   scott at
>> >> >>>> scottcain dot
>> >> >>>> net
>> >> >>>> GMOD Coordinator (http://gmod.org/)
>> >> >>>> 216-392-3087
>> >> >>>> Ontario Institute for Cancer Research
>> >
>> >
>> >
>> >
>> > --
>> > ------------------------------------------------------------------------
>> > Scott Cain, Ph. D.                                   scott at scottcain
>> > dot
>> > net
>> > GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> > Ontario Institute for Cancer Research
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research

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Re: help regarding gbrowse

Scott Cain
Hi Umay,

I'm glad you've gotten it working.

What you're describing with asking for one configuration and getting another is what happens when there is a problem with the configuration that you want.  I don't see anything obvious with the configuration you pasted into the email, but my eyes aren't as good a configuration parser as GBrowse.  A few questions:

Do you see anything in the apache error log that indicates that there is a problem?

Did you add an entry for the new configuration file to /etc/gbrowse/GBrowse.conf?

Scott


On Mon, Sep 22, 2014 at 11:35 PM, umay kulsum <[hidden email]> wrote:
Hi

Thank you scott....got GBrowse installed with git clone...
example database of yeast is also working properly...

but now I have created my own conf file as 114635370.conf in
etc/gbrowse2/gbrowse.conf folder but when I run
http://localhost/cgi-bin/gb2/gbrowse/114635370 it gives the result of
yeast but not my own file
why is it so and what can I do for that??


my conf file is as follows:

[GENERAL]
description   = motifs of 114635370protein
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
               -dir    '/var/www/html/gbrowse2/databases/1/1/4/114635370/'


plugins = BatchDumper FastaDumper
gbrowse root = gbrowse
stylesheet   = gbrowse.css
buttons      = images/buttons
js           = js
tmpimages    = tmp
region segment = 500
initial landmark = 114635370
balloon tips    = 1
drag and drop = 1
cache time    = 1
link          = AUTO
image widths  = 450 640 800 1024
hilite fill    = beige
hilite outline = red
default width = 800
default features = 114635370
max segment     = 500
default segment = 50
zoom levels    = 50 100 200 1000 2000 5000 10000 20000 40000 100000
200000 500000 1000000
show sources   = 1
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
key bgcolor      = beige
examples = 114635370
automatic classes = 114635370


[protein]
feature      = protein
glyph        = so_transcript
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise
height       = 6
description  = 1
balloon hover width = 350
balloon hover = sub { my  = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
     <tr><th rowspan="5" align="left"><br>
     This protein brought to you by <a
href="http://www.expasy.ch">EXPASY</a>.</th>
         <th bgcolor="cyan">Gene </th>
     </tr>
      <tr align='left'><th><a
href="/cgi-bin/gbrowse_details/motif?name=">See protein
details</a></th></tr>
     <tr align='left'><th><a
href="http://www.ncbi.nlm.nih.gov/protein/114635370">Go to
NCBI</a></th></tr>
      </table>

key          = protein
[pattern]
feature      = pattern
glyph        = so_transcript
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise
height       = 6
description  = 1
balloon hover width = 350
balloon hover = sub { my  = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
      <tr><th rowspan="5" align="left"><br>
      This protein brought to you by <a
href="http://www.expasy.ch">EXPASY</a>.</th>
         <th bgcolor="cyan">Gene </th>
      </tr>
      <tr align='left'><th><a
href="/cgi-bin/gbrowse_details/motif?name=">See gene
details</a></th></tr>
     <tr align='left'><th><a
href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
Wikipedia about </a></th></tr>
      <tr align='left'><th><a
href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
      </table>

key           = pattern



[profile]
feature      = profile
glyph        = so_transcript
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise
height       = 6
description  = 0
balloon hover width = 350
balloon hover = sub { my  = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
      <tr><th rowspan="5" align="left"><br>
      This protein brought to you by <a
href="http://www.expasy.ch">EXPASY</a>.</th>
          <th bgcolor="cyan">Gene </th>
     </tr>
      <tr align='left'><th><a
href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
Wikipedia about </a></th></tr>
     <tr align='left'><th><a
href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
     </table>
key          = profile

On Mon, Sep 22, 2014 at 5:36 PM, Scott Cain <[hidden email]> wrote:
> Hi Umay,
>
> I don't really know what the problem is--my guess is that there is a network
> problem.  Can you try from a different network?  Can you clone other things
> from git but just not GBrowse (I would find that pretty strange if it were
> the case)?  Also, in case there is a problem with any of the software
> packages you are using, you should probably run
>
>   sudo apt-get update
>   sudo apt-get upgrade
>
> to make sure your system is up to date.
>
> Scott
>
>
> On Mon, Sep 22, 2014 at 4:17 AM, umay kulsum <[hidden email]> wrote:
>>
>> Hi
>>
>> when I do
>> git clone https://github.com/GMOD/GBrowse.git
>>
>> I get the following error:
>>
>> Cloning into 'GBrowse'...
>> fatal: unable to access 'https://github.com/GMOD/GBrowse.git/':
>> gnutls_handshake() failed: A TLS packet with unexpected length was
>> received.
>>
>> On Thu, Sep 18, 2014 at 7:37 PM, Scott Cain <[hidden email]> wrote:
>> > Hi Umay,
>> >
>> > I suspect you are using Ubuntu 14.04 (you may have already told me
>> > that--I
>> > don't remember).  While working recently on some minor bug fixes for
>> > GBrowse, we discovered that when Ubuntu 14.04 was released, they
>> > dramatically rearranged the file structure for system files, which broke
>> > the
>> > GBrowse installer.  The easiest way to install GBrowse correctly at the
>> > moment is to get a GitHub checkout of the current source and install
>> > that
>> > way.  It's fairly straight forward; this is what you do:
>> >
>> > git clone https://github.com/GMOD/GBrowse.git
>> > cd GBrowse
>> > perl Build.PL  #accepting the defaults should be fine
>> > ./Build
>> > ./Build test
>> > sudo ./Build install
>> >
>> > After doing that you should be able to go to http://localhost/gbrowse2
>> > though the links for sample data sets are written assuming you have
>> > fastcgi
>> > installed (which is a good idea to use, because it makes things faster),
>> > but
>> > if you don't have fastcgi, you should still be able to go to
>> > http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset.  If
>> > that
>> > works, you should be able to proceed with the tutorial as well.
>> >
>> > On Thu, Sep 18, 2014 at 2:15 AM, umay kulsum <[hidden email]>
>> > wrote:
>> >>
>> >> whenever we write localhost it looks for files in /var/www/html
>> >> so I think its looking for /cgi-bin/gb2/gbrowse/yeast in /var/www
>> >>
>> >> On Thu, Sep 18, 2014 at 11:25 AM, umay kulsum <[hidden email]>
>> >> wrote:
>> >> > The apache error log shows :
>> >> >
>> >> > [Thu Sep 18 09:03:14.584273 2014] [core:notice] [pid 10766] AH00094:
>> >> > Command line: '/usr/sbin/apache2'
>> >> >
>> >> >
>> >> > This is the last comment in /var/log/apache2/error.log...... it shows
>> >> > nothing regarding the files not found
>> >> >
>> >> >
>> >> > In the access.log file the last comment is :
>> >> >
>> >> >
>> >> > 127.0.0.1 - - [18/Sep/2014:11:13:58 +0530] "GET
>> >> > /cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513 "-" "Mozilla/5.0 (X11;
>> >> > Ubuntu; Linux x86_64; rv:28.0) Gecko/20100101 Firefox/28.0"
>> >> >
>> >> > On Thu, Sep 18, 2014 at 10:34 AM, Scott Cain <[hidden email]>
>> >> > wrote:
>> >> >> Hi Umay,
>> >> >>
>> >> >> What does it say in the apache error log?  If you're getting a
>> >> >> message
>> >> >> about a file not being found, it will record where it was looking
>> >> >> for the
>> >> >> file. The error log is in /var/log/apache2. The most recent message
>> >> >> is at
>> >> >> the end of the file.
>> >> >>
>> >> >> Scott
>> >> >>
>> >> >>
>> >> >> Sent from my iPhone
>> >> >>
>> >> >>> On Sep 17, 2014, at 11:03 PM, umay kulsum <[hidden email]>
>> >> >>> wrote:
>> >> >>>
>> >> >>> hi
>> >> >>> I have tried http://localhost/cgi-bin/gb2/gbrowse/yeast also but
>> >> >>> again
>> >> >>> its the same the requested url is not found on the server...
>> >> >>> what should I do??
>> >> >>> where am I going wrong??
>> >> >>> can you please tell me how can I start from scratch that is
>> >> >>> uninstall
>> >> >>> and then reinstall....
>> >> >>>
>> >> >>>> On Wed, Sep 17, 2014 at 7:47 PM, Scott Cain <[hidden email]>
>> >> >>>> wrote:
>> >> >>>> Umay,
>> >> >>>>
>> >> >>>> Please "reply-all" so that your replies stay on the GBrowse
>> >> >>>> mailing
>> >> >>>> list.
>> >> >>>>
>> >> >>>> A few things:
>> >> >>>>
>> >> >>>> The url you are using is not correct; it should be
>> >> >>>> http://localhost/cgi-bin/gb2/gbrowse/yeast.  This is linked to
>> >> >>>> from
>> >> >>>> http://localhost/gbrowse2/
>> >> >>>>
>> >> >>>> I don't know why you have two yeast_chr1+2 directories, but only
>> >> >>>> one
>> >> >>>> of them
>> >> >>>> will work.  The typical configuration would be for the one in
>> >> >>>> /var/lib/gbrowse2/databases to work.
>> >> >>>>
>> >> >>>> The cgi-bin directory is not in the /var/www directory when apache
>> >> >>>> is
>> >> >>>> typically configured for ubuntu; it's in /usr/lib/cgi-bin, as it
>> >> >>>> is
>> >> >>>> in your
>> >> >>>> case.
>> >> >>>>
>> >> >>>> Scott
>> >> >>>>
>> >> >>>>
>> >> >>>>> On Wed, Sep 17, 2014 at 4:15 AM, umay kulsum
>> >> >>>>> <[hidden email]>
>> >> >>>>> wrote:
>> >> >>>>>
>> >> >>>>> I have installed GBrowse using the command in ubuntu 14.04
>> >> >>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>> >> >>>>>
>> >> >>>>> I have the following files:
>> >> >>>>> etc/gbrowse2/GBrowse.conf
>> >> >>>>> var/www/gbrowse2/databases where I have the yeast_chr1+2 folder
>> >> >>>>> with
>> >> >>>>> my own data files
>> >> >>>>> usr/lib/cgi-bin/gb2
>> >> >>>>> var/lib/gbrowse2/databases/yeast_chr1+2 with other files
>> >> >>>>>
>> >> >>>>> but still the url http://localhost/cgi-bin/gbrowse2/yeast shows
>> >> >>>>> the
>> >> >>>>> following url was not found on the server
>> >> >>>>>
>> >> >>>>> where is the cgi-bin mentioned in the url located when it is not
>> >> >>>>> in
>> >> >>>>> /var/www/
>> >> >>>>>
>> >> >>>>> On Wed, Sep 17, 2014 at 8:54 AM, umay kulsum
>> >> >>>>> <[hidden email]>
>> >> >>>>> wrote:
>> >> >>>>>> Hi
>> >> >>>>>> I have installed GBrowse using the command in ubuntu 14.04
>> >> >>>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>> >> >>>>>> but when I point my browser to
>> >> >>>>>> http://localhost/cgi-bin/gbrowse2/yeast, it shows the following
>> >> >>>>>> url
>> >> >>>>>> is
>> >> >>>>>> not found on this server..
>> >> >>>>>> where is the cgi-bin mentioned in the url located when it is not
>> >> >>>>>> in
>> >> >>>>>> /var/www/
>> >> >>>>>>
>> >> >>>>>>> On Tue, Sep 16, 2014 at 2:28 AM, Scott Cain
>> >> >>>>>>> <[hidden email]>
>> >> >>>>>>> wrote:
>> >> >>>>>>> Hi Umay,
>> >> >>>>>>>
>> >> >>>>>>> Can you please tell us what you done and where you think the
>> >> >>>>>>> process
>> >> >>>>>>> has failed?  For instance, what do you see when you go to the
>> >> >>>>>>> built in
>> >> >>>>>>> sample yeast data set?
>> >> >>>>>>>
>> >> >>>>>>> Scott
>> >> >>>>>>>
>> >> >>>>>>> Sent from my iPhone
>> >> >>>>>>>
>> >> >>>>>>>> On Sep 11, 2014, at 11:41 PM, umay kulsum
>> >> >>>>>>>> <[hidden email]>
>> >> >>>>>>>> wrote:
>> >> >>>>>>>>
>> >> >>>>>>>> I have been trying to install and invoke GBrowse since a month
>> >> >>>>>>>> but to
>> >> >>>>>>>> no result....
>> >> >>>>>>>> can someone help me regarding the installation process.
>> >> >>>>>>>>
>> >> >>>>>>>>
>> >> >>>>>>>>
>> >> >>>>>>>>
>> >> >>>>>>>> ------------------------------------------------------------------------------
>> >> >>>>>>>> Want excitement?
>> >> >>>>>>>> Manually upgrade your production database.
>> >> >>>>>>>> When you want reliability, choose Perforce
>> >> >>>>>>>> Perforce version control. Predictably reliable.
>> >> >>>>>>>>
>> >> >>>>>>>>
>> >> >>>>>>>>
>> >> >>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
>> >> >>>>>>>> _______________________________________________
>> >> >>>>>>>> Gmod-gbrowse mailing list
>> >> >>>>>>>> [hidden email]
>> >> >>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >> >>>>
>> >> >>>>
>> >> >>>>
>> >> >>>>
>> >> >>>> --
>> >> >>>>
>> >> >>>>
>> >> >>>> ------------------------------------------------------------------------
>> >> >>>> Scott Cain, Ph. D.                                   scott at
>> >> >>>> scottcain dot
>> >> >>>> net
>> >> >>>> GMOD Coordinator (http://gmod.org/)
>> >> >>>> <a href="tel:216-392-3087" value="+12163923087">216-392-3087
>> >> >>>> Ontario Institute for Cancer Research
>> >
>> >
>> >
>> >
>> > --
>> > ------------------------------------------------------------------------
>> > Scott Cain, Ph. D.                                   scott at scottcain
>> > dot
>> > net
>> > GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
>> > Ontario Institute for Cancer Research
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
> Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: help regarding gbrowse

umay kulsum
Hi

The error log shows:
[cgi:error] [pid 17807] [client 127.0.0.1:34119] AH01215: STACK:
/usr/lib/cgi-bin/gb2/gbrowse:55

yes I added the entry to /etc/gbrowse/GBrowse.conf

On Tue, Sep 23, 2014 at 6:52 PM, Scott Cain <[hidden email]> wrote:

> Hi Umay,
>
> I'm glad you've gotten it working.
>
> What you're describing with asking for one configuration and getting another
> is what happens when there is a problem with the configuration that you
> want.  I don't see anything obvious with the configuration you pasted into
> the email, but my eyes aren't as good a configuration parser as GBrowse.  A
> few questions:
>
> Do you see anything in the apache error log that indicates that there is a
> problem?
>
> Did you add an entry for the new configuration file to
> /etc/gbrowse/GBrowse.conf?
>
> Scott
>
>
> On Mon, Sep 22, 2014 at 11:35 PM, umay kulsum <[hidden email]> wrote:
>>
>> Hi
>>
>> Thank you scott....got GBrowse installed with git clone...
>> example database of yeast is also working properly...
>>
>> but now I have created my own conf file as 114635370.conf in
>> etc/gbrowse2/gbrowse.conf folder but when I run
>> http://localhost/cgi-bin/gb2/gbrowse/114635370 it gives the result of
>> yeast but not my own file
>> why is it so and what can I do for that??
>>
>>
>> my conf file is as follows:
>>
>> [GENERAL]
>> description   = motifs of 114635370protein
>> db_adaptor    = Bio::DB::SeqFeature::Store
>> db_args       = -adaptor memory
>>                -dir    '/var/www/html/gbrowse2/databases/1/1/4/114635370/'
>>
>>
>> plugins = BatchDumper FastaDumper
>> gbrowse root = gbrowse
>> stylesheet   = gbrowse.css
>> buttons      = images/buttons
>> js           = js
>> tmpimages    = tmp
>> region segment = 500
>> initial landmark = 114635370
>> balloon tips    = 1
>> drag and drop = 1
>> cache time    = 1
>> link          = AUTO
>> image widths  = 450 640 800 1024
>> hilite fill    = beige
>> hilite outline = red
>> default width = 800
>> default features = 114635370
>> max segment     = 500
>> default segment = 50
>> zoom levels    = 50 100 200 1000 2000 5000 10000 20000 40000 100000
>> 200000 500000 1000000
>> show sources   = 1
>> overview bgcolor = lightgrey
>> detailed bgcolor = lightgoldenrodyellow
>> key bgcolor      = beige
>> examples = 114635370
>> automatic classes = 114635370
>>
>>
>> [protein]
>> feature      = protein
>> glyph        = so_transcript
>> bgcolor      = yellow
>> forwardcolor = yellow
>> reversecolor = turquoise
>> height       = 6
>> description  = 1
>> balloon hover width = 350
>> balloon hover = sub { my  = shift; return join ' ',->notes }
>> balloon click width = 450
>> balloon click = <table>
>>      <tr><th rowspan="5" align="left"><br>
>>      This protein brought to you by <a
>> href="http://www.expasy.ch">EXPASY</a>.</th>
>>          <th bgcolor="cyan">Gene </th>
>>      </tr>
>>       <tr align='left'><th><a
>> href="/cgi-bin/gbrowse_details/motif?name=">See protein
>> details</a></th></tr>
>>      <tr align='left'><th><a
>> href="http://www.ncbi.nlm.nih.gov/protein/114635370">Go to
>> NCBI</a></th></tr>
>>       </table>
>>
>> key          = protein
>> [pattern]
>> feature      = pattern
>> glyph        = so_transcript
>> bgcolor      = yellow
>> forwardcolor = yellow
>> reversecolor = turquoise
>> height       = 6
>> description  = 1
>> balloon hover width = 350
>> balloon hover = sub { my  = shift; return join ' ',->notes }
>> balloon click width = 450
>> balloon click = <table>
>>       <tr><th rowspan="5" align="left"><br>
>>       This protein brought to you by <a
>> href="http://www.expasy.ch">EXPASY</a>.</th>
>>          <th bgcolor="cyan">Gene </th>
>>       </tr>
>>       <tr align='left'><th><a
>> href="/cgi-bin/gbrowse_details/motif?name=">See gene
>> details</a></th></tr>
>>      <tr align='left'><th><a
>> href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
>> Wikipedia about </a></th></tr>
>>       <tr align='left'><th><a
>> href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
>>       </table>
>>
>> key           = pattern
>>
>>
>>
>> [profile]
>> feature      = profile
>> glyph        = so_transcript
>> bgcolor      = yellow
>> forwardcolor = yellow
>> reversecolor = turquoise
>> height       = 6
>> description  = 0
>> balloon hover width = 350
>> balloon hover = sub { my  = shift; return join ' ',->notes }
>> balloon click width = 450
>> balloon click = <table>
>>       <tr><th rowspan="5" align="left"><br>
>>       This protein brought to you by <a
>> href="http://www.expasy.ch">EXPASY</a>.</th>
>>           <th bgcolor="cyan">Gene </th>
>>      </tr>
>>       <tr align='left'><th><a
>> href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
>> Wikipedia about </a></th></tr>
>>      <tr align='left'><th><a
>> href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
>>      </table>
>> key          = profile
>>
>> On Mon, Sep 22, 2014 at 5:36 PM, Scott Cain <[hidden email]> wrote:
>> > Hi Umay,
>> >
>> > I don't really know what the problem is--my guess is that there is a
>> > network
>> > problem.  Can you try from a different network?  Can you clone other
>> > things
>> > from git but just not GBrowse (I would find that pretty strange if it
>> > were
>> > the case)?  Also, in case there is a problem with any of the software
>> > packages you are using, you should probably run
>> >
>> >   sudo apt-get update
>> >   sudo apt-get upgrade
>> >
>> > to make sure your system is up to date.
>> >
>> > Scott
>> >
>> >
>> > On Mon, Sep 22, 2014 at 4:17 AM, umay kulsum <[hidden email]>
>> > wrote:
>> >>
>> >> Hi
>> >>
>> >> when I do
>> >> git clone https://github.com/GMOD/GBrowse.git
>> >>
>> >> I get the following error:
>> >>
>> >> Cloning into 'GBrowse'...
>> >> fatal: unable to access 'https://github.com/GMOD/GBrowse.git/':
>> >> gnutls_handshake() failed: A TLS packet with unexpected length was
>> >> received.
>> >>
>> >> On Thu, Sep 18, 2014 at 7:37 PM, Scott Cain <[hidden email]>
>> >> wrote:
>> >> > Hi Umay,
>> >> >
>> >> > I suspect you are using Ubuntu 14.04 (you may have already told me
>> >> > that--I
>> >> > don't remember).  While working recently on some minor bug fixes for
>> >> > GBrowse, we discovered that when Ubuntu 14.04 was released, they
>> >> > dramatically rearranged the file structure for system files, which
>> >> > broke
>> >> > the
>> >> > GBrowse installer.  The easiest way to install GBrowse correctly at
>> >> > the
>> >> > moment is to get a GitHub checkout of the current source and install
>> >> > that
>> >> > way.  It's fairly straight forward; this is what you do:
>> >> >
>> >> > git clone https://github.com/GMOD/GBrowse.git
>> >> > cd GBrowse
>> >> > perl Build.PL  #accepting the defaults should be fine
>> >> > ./Build
>> >> > ./Build test
>> >> > sudo ./Build install
>> >> >
>> >> > After doing that you should be able to go to
>> >> > http://localhost/gbrowse2
>> >> > though the links for sample data sets are written assuming you have
>> >> > fastcgi
>> >> > installed (which is a good idea to use, because it makes things
>> >> > faster),
>> >> > but
>> >> > if you don't have fastcgi, you should still be able to go to
>> >> > http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset.
>> >> > If
>> >> > that
>> >> > works, you should be able to proceed with the tutorial as well.
>> >> >
>> >> > On Thu, Sep 18, 2014 at 2:15 AM, umay kulsum <[hidden email]>
>> >> > wrote:
>> >> >>
>> >> >> whenever we write localhost it looks for files in /var/www/html
>> >> >> so I think its looking for /cgi-bin/gb2/gbrowse/yeast in /var/www
>> >> >>
>> >> >> On Thu, Sep 18, 2014 at 11:25 AM, umay kulsum
>> >> >> <[hidden email]>
>> >> >> wrote:
>> >> >> > The apache error log shows :
>> >> >> >
>> >> >> > [Thu Sep 18 09:03:14.584273 2014] [core:notice] [pid 10766]
>> >> >> > AH00094:
>> >> >> > Command line: '/usr/sbin/apache2'
>> >> >> >
>> >> >> >
>> >> >> > This is the last comment in /var/log/apache2/error.log...... it
>> >> >> > shows
>> >> >> > nothing regarding the files not found
>> >> >> >
>> >> >> >
>> >> >> > In the access.log file the last comment is :
>> >> >> >
>> >> >> >
>> >> >> > 127.0.0.1 - - [18/Sep/2014:11:13:58 +0530] "GET
>> >> >> > /cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513 "-" "Mozilla/5.0
>> >> >> > (X11;
>> >> >> > Ubuntu; Linux x86_64; rv:28.0) Gecko/20100101 Firefox/28.0"
>> >> >> >
>> >> >> > On Thu, Sep 18, 2014 at 10:34 AM, Scott Cain <[hidden email]>
>> >> >> > wrote:
>> >> >> >> Hi Umay,
>> >> >> >>
>> >> >> >> What does it say in the apache error log?  If you're getting a
>> >> >> >> message
>> >> >> >> about a file not being found, it will record where it was looking
>> >> >> >> for the
>> >> >> >> file. The error log is in /var/log/apache2. The most recent
>> >> >> >> message
>> >> >> >> is at
>> >> >> >> the end of the file.
>> >> >> >>
>> >> >> >> Scott
>> >> >> >>
>> >> >> >>
>> >> >> >> Sent from my iPhone
>> >> >> >>
>> >> >> >>> On Sep 17, 2014, at 11:03 PM, umay kulsum
>> >> >> >>> <[hidden email]>
>> >> >> >>> wrote:
>> >> >> >>>
>> >> >> >>> hi
>> >> >> >>> I have tried http://localhost/cgi-bin/gb2/gbrowse/yeast also but
>> >> >> >>> again
>> >> >> >>> its the same the requested url is not found on the server...
>> >> >> >>> what should I do??
>> >> >> >>> where am I going wrong??
>> >> >> >>> can you please tell me how can I start from scratch that is
>> >> >> >>> uninstall
>> >> >> >>> and then reinstall....
>> >> >> >>>
>> >> >> >>>> On Wed, Sep 17, 2014 at 7:47 PM, Scott Cain
>> >> >> >>>> <[hidden email]>
>> >> >> >>>> wrote:
>> >> >> >>>> Umay,
>> >> >> >>>>
>> >> >> >>>> Please "reply-all" so that your replies stay on the GBrowse
>> >> >> >>>> mailing
>> >> >> >>>> list.
>> >> >> >>>>
>> >> >> >>>> A few things:
>> >> >> >>>>
>> >> >> >>>> The url you are using is not correct; it should be
>> >> >> >>>> http://localhost/cgi-bin/gb2/gbrowse/yeast.  This is linked to
>> >> >> >>>> from
>> >> >> >>>> http://localhost/gbrowse2/
>> >> >> >>>>
>> >> >> >>>> I don't know why you have two yeast_chr1+2 directories, but
>> >> >> >>>> only
>> >> >> >>>> one
>> >> >> >>>> of them
>> >> >> >>>> will work.  The typical configuration would be for the one in
>> >> >> >>>> /var/lib/gbrowse2/databases to work.
>> >> >> >>>>
>> >> >> >>>> The cgi-bin directory is not in the /var/www directory when
>> >> >> >>>> apache
>> >> >> >>>> is
>> >> >> >>>> typically configured for ubuntu; it's in /usr/lib/cgi-bin, as
>> >> >> >>>> it
>> >> >> >>>> is
>> >> >> >>>> in your
>> >> >> >>>> case.
>> >> >> >>>>
>> >> >> >>>> Scott
>> >> >> >>>>
>> >> >> >>>>
>> >> >> >>>>> On Wed, Sep 17, 2014 at 4:15 AM, umay kulsum
>> >> >> >>>>> <[hidden email]>
>> >> >> >>>>> wrote:
>> >> >> >>>>>
>> >> >> >>>>> I have installed GBrowse using the command in ubuntu 14.04
>> >> >> >>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>> >> >> >>>>>
>> >> >> >>>>> I have the following files:
>> >> >> >>>>> etc/gbrowse2/GBrowse.conf
>> >> >> >>>>> var/www/gbrowse2/databases where I have the yeast_chr1+2
>> >> >> >>>>> folder
>> >> >> >>>>> with
>> >> >> >>>>> my own data files
>> >> >> >>>>> usr/lib/cgi-bin/gb2
>> >> >> >>>>> var/lib/gbrowse2/databases/yeast_chr1+2 with other files
>> >> >> >>>>>
>> >> >> >>>>> but still the url http://localhost/cgi-bin/gbrowse2/yeast
>> >> >> >>>>> shows
>> >> >> >>>>> the
>> >> >> >>>>> following url was not found on the server
>> >> >> >>>>>
>> >> >> >>>>> where is the cgi-bin mentioned in the url located when it is
>> >> >> >>>>> not
>> >> >> >>>>> in
>> >> >> >>>>> /var/www/
>> >> >> >>>>>
>> >> >> >>>>> On Wed, Sep 17, 2014 at 8:54 AM, umay kulsum
>> >> >> >>>>> <[hidden email]>
>> >> >> >>>>> wrote:
>> >> >> >>>>>> Hi
>> >> >> >>>>>> I have installed GBrowse using the command in ubuntu 14.04
>> >> >> >>>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>> >> >> >>>>>> but when I point my browser to
>> >> >> >>>>>> http://localhost/cgi-bin/gbrowse2/yeast, it shows the
>> >> >> >>>>>> following
>> >> >> >>>>>> url
>> >> >> >>>>>> is
>> >> >> >>>>>> not found on this server..
>> >> >> >>>>>> where is the cgi-bin mentioned in the url located when it is
>> >> >> >>>>>> not
>> >> >> >>>>>> in
>> >> >> >>>>>> /var/www/
>> >> >> >>>>>>
>> >> >> >>>>>>> On Tue, Sep 16, 2014 at 2:28 AM, Scott Cain
>> >> >> >>>>>>> <[hidden email]>
>> >> >> >>>>>>> wrote:
>> >> >> >>>>>>> Hi Umay,
>> >> >> >>>>>>>
>> >> >> >>>>>>> Can you please tell us what you done and where you think the
>> >> >> >>>>>>> process
>> >> >> >>>>>>> has failed?  For instance, what do you see when you go to
>> >> >> >>>>>>> the
>> >> >> >>>>>>> built in
>> >> >> >>>>>>> sample yeast data set?
>> >> >> >>>>>>>
>> >> >> >>>>>>> Scott
>> >> >> >>>>>>>
>> >> >> >>>>>>> Sent from my iPhone
>> >> >> >>>>>>>
>> >> >> >>>>>>>> On Sep 11, 2014, at 11:41 PM, umay kulsum
>> >> >> >>>>>>>> <[hidden email]>
>> >> >> >>>>>>>> wrote:
>> >> >> >>>>>>>>
>> >> >> >>>>>>>> I have been trying to install and invoke GBrowse since a
>> >> >> >>>>>>>> month
>> >> >> >>>>>>>> but to
>> >> >> >>>>>>>> no result....
>> >> >> >>>>>>>> can someone help me regarding the installation process.
>> >> >> >>>>>>>>
>> >> >> >>>>>>>>
>> >> >> >>>>>>>>
>> >> >> >>>>>>>>
>> >> >> >>>>>>>>
>> >> >> >>>>>>>> ------------------------------------------------------------------------------
>> >> >> >>>>>>>> Want excitement?
>> >> >> >>>>>>>> Manually upgrade your production database.
>> >> >> >>>>>>>> When you want reliability, choose Perforce
>> >> >> >>>>>>>> Perforce version control. Predictably reliable.
>> >> >> >>>>>>>>
>> >> >> >>>>>>>>
>> >> >> >>>>>>>>
>> >> >> >>>>>>>>
>> >> >> >>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
>> >> >> >>>>>>>> _______________________________________________
>> >> >> >>>>>>>> Gmod-gbrowse mailing list
>> >> >> >>>>>>>> [hidden email]
>> >> >> >>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >> >> >>>>
>> >> >> >>>>
>> >> >> >>>>
>> >> >> >>>>
>> >> >> >>>> --
>> >> >> >>>>
>> >> >> >>>>
>> >> >> >>>>
>> >> >> >>>> ------------------------------------------------------------------------
>> >> >> >>>> Scott Cain, Ph. D.                                   scott at
>> >> >> >>>> scottcain dot
>> >> >> >>>> net
>> >> >> >>>> GMOD Coordinator (http://gmod.org/)
>> >> >> >>>> 216-392-3087
>> >> >> >>>> Ontario Institute for Cancer Research
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> >
>> >> > ------------------------------------------------------------------------
>> >> > Scott Cain, Ph. D.                                   scott at
>> >> > scottcain
>> >> > dot
>> >> > net
>> >> > GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> > Ontario Institute for Cancer Research
>> >
>> >
>> >
>> >
>> > --
>> > ------------------------------------------------------------------------
>> > Scott Cain, Ph. D.                                   scott at scottcain
>> > dot
>> > net
>> > GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> > Ontario Institute for Cancer Research
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research

------------------------------------------------------------------------------
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Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
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Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
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Re: help regarding gbrowse

umay kulsum
hi Scott

I have created a script gbtry.php which is as follows:

<?php
$ourFileName = "/etc/gbrowse2/gbrowse.conf/".10190714.".conf";
$ourFileHandle = fopen($ourFileName, 'w') or die("can't open file");
$p="[GENERAL]
description   = motifs of ".21105857."protein
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
               -dir    '/var/www/html/gbrowse2/databases/10190714'


plugins = BatchDumper FastaDumper
gbrowse root = gbrowse
stylesheet   = gbrowse.css
buttons      = images/buttons
js           = js
tmpimages    = tmp
region segment = 500
initial landmark = \".21105857.\"
balloon tips    = 1
drag and drop = 1
cache time    = 1
link          = AUTO
image widths  = 450 640 800 1024
hilite fill    = beige
hilite outline = red
default width = 800
default features = \".21105857.\"
max segment     = 500
default segment = 50
zoom levels    = 50 100 200 1000 2000 5000 10000 20000 40000 100000
200000 500000 1000000
show sources   = 1
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
key bgcolor      = beige
examples =\".21105857.\"
automatic classes = \".21105857.\"


[protein]
feature      = protein
glyph        = so_transcript
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise
height       = 6
description  = 1
balloon hover width = 350
balloon hover = sub { my  = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
     <tr><th rowspan="5" align=\"left\"><br>
     This protein brought to you by <a
href=\"http://www.expasy.ch\">EXPASY</a>.</th>
         <th bgcolor=\"cyan\">Gene </th>
     </tr>
      <tr align='left'><th><a
href=\"/cgi-bin/gbrowse_details/motif?name=\">See protein
details</a></th></tr>
     <tr align='left'><th><a
href=\"http://www.ncbi.nlm.nih.gov/protein/\".21105857."">Go to
NCBI</a></th></tr>
      </table>

key          = protein
[pattern]
feature      = pattern
glyph        = so_transcript
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise
height       = 6
description  = 1
balloon hover width = 350
balloon hover = sub { my  = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
      <tr><th rowspan="5" align=\"left\"><br>
      This protein brought to you by <a
href=\"http://www.expasy.ch\">EXPASY</a>.</th>
         <th bgcolor=\"cyan\">Gene </th>
      </tr>
      <tr align='left'><th><a
href=\"/cgi-bin/gbrowse_details/motif?name=\">See gene
details</a></th></tr>
     <tr align='left'><th><a
href=\"http://en.wikipedia.org/wiki/Special:Search?search=\">Ask
Wikipedia about </a></th></tr>
      <tr align='left'><th><a
href=\"http://www.google.com/search?q=\">Ask Google about
</a></th></tr>
      </table>

key           = pattern



[profile]
feature      = profile
glyph        = so_transcript
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise
height       = 6
description  = 0
balloon hover width = 350
balloon hover = sub { my  = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
      <tr><th rowspan="5" align=\"left\"><br>
      This protein brought to you by <a
href=\"http://www.expasy.ch\">EXPASY</a>.</th>
          <th bgcolor=\"cyan\">Gene </th>
     </tr>
      <tr align='left'><th><a
href=\"http://en.wikipedia.org/wiki/Special:Search?search=/\">Ask
Wikipedia about </a></th></tr>
     <tr align='left'><th><a
href=\"http://www.google.com/search?q=\">Ask Google about
</a></th></tr>
     </table>
key          = profile";
fwrite($ourFileHandle, $p);

$url="http://localhost/cgi-bin/gb2/gbrowse/".10190714;
echo "<br><iframe src =".$url." width="1000" height="700" >
</iframe>";}
?>



but when I point my browser to http://localhost/cgi-bin/gb2/gbrowse/10190714

I get the attached snapshot

On Wed, Sep 24, 2014 at 9:05 AM, umay kulsum <[hidden email]> wrote:

> Hi
>
> The error log shows:
> [cgi:error] [pid 17807] [client 127.0.0.1:34119] AH01215: STACK:
> /usr/lib/cgi-bin/gb2/gbrowse:55
>
> yes I added the entry to /etc/gbrowse/GBrowse.conf
>
> On Tue, Sep 23, 2014 at 6:52 PM, Scott Cain <[hidden email]> wrote:
>> Hi Umay,
>>
>> I'm glad you've gotten it working.
>>
>> What you're describing with asking for one configuration and getting another
>> is what happens when there is a problem with the configuration that you
>> want.  I don't see anything obvious with the configuration you pasted into
>> the email, but my eyes aren't as good a configuration parser as GBrowse.  A
>> few questions:
>>
>> Do you see anything in the apache error log that indicates that there is a
>> problem?
>>
>> Did you add an entry for the new configuration file to
>> /etc/gbrowse/GBrowse.conf?
>>
>> Scott
>>
>>
>> On Mon, Sep 22, 2014 at 11:35 PM, umay kulsum <[hidden email]> wrote:
>>>
>>> Hi
>>>
>>> Thank you scott....got GBrowse installed with git clone...
>>> example database of yeast is also working properly...
>>>
>>> but now I have created my own conf file as 114635370.conf in
>>> etc/gbrowse2/gbrowse.conf folder but when I run
>>> http://localhost/cgi-bin/gb2/gbrowse/114635370 it gives the result of
>>> yeast but not my own file
>>> why is it so and what can I do for that??
>>>
>>>
>>> my conf file is as follows:
>>>
>>> [GENERAL]
>>> description   = motifs of 114635370protein
>>> db_adaptor    = Bio::DB::SeqFeature::Store
>>> db_args       = -adaptor memory
>>>                -dir    '/var/www/html/gbrowse2/databases/1/1/4/114635370/'
>>>
>>>
>>> plugins = BatchDumper FastaDumper
>>> gbrowse root = gbrowse
>>> stylesheet   = gbrowse.css
>>> buttons      = images/buttons
>>> js           = js
>>> tmpimages    = tmp
>>> region segment = 500
>>> initial landmark = 114635370
>>> balloon tips    = 1
>>> drag and drop = 1
>>> cache time    = 1
>>> link          = AUTO
>>> image widths  = 450 640 800 1024
>>> hilite fill    = beige
>>> hilite outline = red
>>> default width = 800
>>> default features = 114635370
>>> max segment     = 500
>>> default segment = 50
>>> zoom levels    = 50 100 200 1000 2000 5000 10000 20000 40000 100000
>>> 200000 500000 1000000
>>> show sources   = 1
>>> overview bgcolor = lightgrey
>>> detailed bgcolor = lightgoldenrodyellow
>>> key bgcolor      = beige
>>> examples = 114635370
>>> automatic classes = 114635370
>>>
>>>
>>> [protein]
>>> feature      = protein
>>> glyph        = so_transcript
>>> bgcolor      = yellow
>>> forwardcolor = yellow
>>> reversecolor = turquoise
>>> height       = 6
>>> description  = 1
>>> balloon hover width = 350
>>> balloon hover = sub { my  = shift; return join ' ',->notes }
>>> balloon click width = 450
>>> balloon click = <table>
>>>      <tr><th rowspan="5" align="left"><br>
>>>      This protein brought to you by <a
>>> href="http://www.expasy.ch">EXPASY</a>.</th>
>>>          <th bgcolor="cyan">Gene </th>
>>>      </tr>
>>>       <tr align='left'><th><a
>>> href="/cgi-bin/gbrowse_details/motif?name=">See protein
>>> details</a></th></tr>
>>>      <tr align='left'><th><a
>>> href="http://www.ncbi.nlm.nih.gov/protein/114635370">Go to
>>> NCBI</a></th></tr>
>>>       </table>
>>>
>>> key          = protein
>>> [pattern]
>>> feature      = pattern
>>> glyph        = so_transcript
>>> bgcolor      = yellow
>>> forwardcolor = yellow
>>> reversecolor = turquoise
>>> height       = 6
>>> description  = 1
>>> balloon hover width = 350
>>> balloon hover = sub { my  = shift; return join ' ',->notes }
>>> balloon click width = 450
>>> balloon click = <table>
>>>       <tr><th rowspan="5" align="left"><br>
>>>       This protein brought to you by <a
>>> href="http://www.expasy.ch">EXPASY</a>.</th>
>>>          <th bgcolor="cyan">Gene </th>
>>>       </tr>
>>>       <tr align='left'><th><a
>>> href="/cgi-bin/gbrowse_details/motif?name=">See gene
>>> details</a></th></tr>
>>>      <tr align='left'><th><a
>>> href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
>>> Wikipedia about </a></th></tr>
>>>       <tr align='left'><th><a
>>> href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
>>>       </table>
>>>
>>> key           = pattern
>>>
>>>
>>>
>>> [profile]
>>> feature      = profile
>>> glyph        = so_transcript
>>> bgcolor      = yellow
>>> forwardcolor = yellow
>>> reversecolor = turquoise
>>> height       = 6
>>> description  = 0
>>> balloon hover width = 350
>>> balloon hover = sub { my  = shift; return join ' ',->notes }
>>> balloon click width = 450
>>> balloon click = <table>
>>>       <tr><th rowspan="5" align="left"><br>
>>>       This protein brought to you by <a
>>> href="http://www.expasy.ch">EXPASY</a>.</th>
>>>           <th bgcolor="cyan">Gene </th>
>>>      </tr>
>>>       <tr align='left'><th><a
>>> href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
>>> Wikipedia about </a></th></tr>
>>>      <tr align='left'><th><a
>>> href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
>>>      </table>
>>> key          = profile
>>>
>>> On Mon, Sep 22, 2014 at 5:36 PM, Scott Cain <[hidden email]> wrote:
>>> > Hi Umay,
>>> >
>>> > I don't really know what the problem is--my guess is that there is a
>>> > network
>>> > problem.  Can you try from a different network?  Can you clone other
>>> > things
>>> > from git but just not GBrowse (I would find that pretty strange if it
>>> > were
>>> > the case)?  Also, in case there is a problem with any of the software
>>> > packages you are using, you should probably run
>>> >
>>> >   sudo apt-get update
>>> >   sudo apt-get upgrade
>>> >
>>> > to make sure your system is up to date.
>>> >
>>> > Scott
>>> >
>>> >
>>> > On Mon, Sep 22, 2014 at 4:17 AM, umay kulsum <[hidden email]>
>>> > wrote:
>>> >>
>>> >> Hi
>>> >>
>>> >> when I do
>>> >> git clone https://github.com/GMOD/GBrowse.git
>>> >>
>>> >> I get the following error:
>>> >>
>>> >> Cloning into 'GBrowse'...
>>> >> fatal: unable to access 'https://github.com/GMOD/GBrowse.git/':
>>> >> gnutls_handshake() failed: A TLS packet with unexpected length was
>>> >> received.
>>> >>
>>> >> On Thu, Sep 18, 2014 at 7:37 PM, Scott Cain <[hidden email]>
>>> >> wrote:
>>> >> > Hi Umay,
>>> >> >
>>> >> > I suspect you are using Ubuntu 14.04 (you may have already told me
>>> >> > that--I
>>> >> > don't remember).  While working recently on some minor bug fixes for
>>> >> > GBrowse, we discovered that when Ubuntu 14.04 was released, they
>>> >> > dramatically rearranged the file structure for system files, which
>>> >> > broke
>>> >> > the
>>> >> > GBrowse installer.  The easiest way to install GBrowse correctly at
>>> >> > the
>>> >> > moment is to get a GitHub checkout of the current source and install
>>> >> > that
>>> >> > way.  It's fairly straight forward; this is what you do:
>>> >> >
>>> >> > git clone https://github.com/GMOD/GBrowse.git
>>> >> > cd GBrowse
>>> >> > perl Build.PL  #accepting the defaults should be fine
>>> >> > ./Build
>>> >> > ./Build test
>>> >> > sudo ./Build install
>>> >> >
>>> >> > After doing that you should be able to go to
>>> >> > http://localhost/gbrowse2
>>> >> > though the links for sample data sets are written assuming you have
>>> >> > fastcgi
>>> >> > installed (which is a good idea to use, because it makes things
>>> >> > faster),
>>> >> > but
>>> >> > if you don't have fastcgi, you should still be able to go to
>>> >> > http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset.
>>> >> > If
>>> >> > that
>>> >> > works, you should be able to proceed with the tutorial as well.
>>> >> >
>>> >> > On Thu, Sep 18, 2014 at 2:15 AM, umay kulsum <[hidden email]>
>>> >> > wrote:
>>> >> >>
>>> >> >> whenever we write localhost it looks for files in /var/www/html
>>> >> >> so I think its looking for /cgi-bin/gb2/gbrowse/yeast in /var/www
>>> >> >>
>>> >> >> On Thu, Sep 18, 2014 at 11:25 AM, umay kulsum
>>> >> >> <[hidden email]>
>>> >> >> wrote:
>>> >> >> > The apache error log shows :
>>> >> >> >
>>> >> >> > [Thu Sep 18 09:03:14.584273 2014] [core:notice] [pid 10766]
>>> >> >> > AH00094:
>>> >> >> > Command line: '/usr/sbin/apache2'
>>> >> >> >
>>> >> >> >
>>> >> >> > This is the last comment in /var/log/apache2/error.log...... it
>>> >> >> > shows
>>> >> >> > nothing regarding the files not found
>>> >> >> >
>>> >> >> >
>>> >> >> > In the access.log file the last comment is :
>>> >> >> >
>>> >> >> >
>>> >> >> > 127.0.0.1 - - [18/Sep/2014:11:13:58 +0530] "GET
>>> >> >> > /cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513 "-" "Mozilla/5.0
>>> >> >> > (X11;
>>> >> >> > Ubuntu; Linux x86_64; rv:28.0) Gecko/20100101 Firefox/28.0"
>>> >> >> >
>>> >> >> > On Thu, Sep 18, 2014 at 10:34 AM, Scott Cain <[hidden email]>
>>> >> >> > wrote:
>>> >> >> >> Hi Umay,
>>> >> >> >>
>>> >> >> >> What does it say in the apache error log?  If you're getting a
>>> >> >> >> message
>>> >> >> >> about a file not being found, it will record where it was looking
>>> >> >> >> for the
>>> >> >> >> file. The error log is in /var/log/apache2. The most recent
>>> >> >> >> message
>>> >> >> >> is at
>>> >> >> >> the end of the file.
>>> >> >> >>
>>> >> >> >> Scott
>>> >> >> >>
>>> >> >> >>
>>> >> >> >> Sent from my iPhone
>>> >> >> >>
>>> >> >> >>> On Sep 17, 2014, at 11:03 PM, umay kulsum
>>> >> >> >>> <[hidden email]>
>>> >> >> >>> wrote:
>>> >> >> >>>
>>> >> >> >>> hi
>>> >> >> >>> I have tried http://localhost/cgi-bin/gb2/gbrowse/yeast also but
>>> >> >> >>> again
>>> >> >> >>> its the same the requested url is not found on the server...
>>> >> >> >>> what should I do??
>>> >> >> >>> where am I going wrong??
>>> >> >> >>> can you please tell me how can I start from scratch that is
>>> >> >> >>> uninstall
>>> >> >> >>> and then reinstall....
>>> >> >> >>>
>>> >> >> >>>> On Wed, Sep 17, 2014 at 7:47 PM, Scott Cain
>>> >> >> >>>> <[hidden email]>
>>> >> >> >>>> wrote:
>>> >> >> >>>> Umay,
>>> >> >> >>>>
>>> >> >> >>>> Please "reply-all" so that your replies stay on the GBrowse
>>> >> >> >>>> mailing
>>> >> >> >>>> list.
>>> >> >> >>>>
>>> >> >> >>>> A few things:
>>> >> >> >>>>
>>> >> >> >>>> The url you are using is not correct; it should be
>>> >> >> >>>> http://localhost/cgi-bin/gb2/gbrowse/yeast.  This is linked to
>>> >> >> >>>> from
>>> >> >> >>>> http://localhost/gbrowse2/
>>> >> >> >>>>
>>> >> >> >>>> I don't know why you have two yeast_chr1+2 directories, but
>>> >> >> >>>> only
>>> >> >> >>>> one
>>> >> >> >>>> of them
>>> >> >> >>>> will work.  The typical configuration would be for the one in
>>> >> >> >>>> /var/lib/gbrowse2/databases to work.
>>> >> >> >>>>
>>> >> >> >>>> The cgi-bin directory is not in the /var/www directory when
>>> >> >> >>>> apache
>>> >> >> >>>> is
>>> >> >> >>>> typically configured for ubuntu; it's in /usr/lib/cgi-bin, as
>>> >> >> >>>> it
>>> >> >> >>>> is
>>> >> >> >>>> in your
>>> >> >> >>>> case.
>>> >> >> >>>>
>>> >> >> >>>> Scott
>>> >> >> >>>>
>>> >> >> >>>>
>>> >> >> >>>>> On Wed, Sep 17, 2014 at 4:15 AM, umay kulsum
>>> >> >> >>>>> <[hidden email]>
>>> >> >> >>>>> wrote:
>>> >> >> >>>>>
>>> >> >> >>>>> I have installed GBrowse using the command in ubuntu 14.04
>>> >> >> >>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>>> >> >> >>>>>
>>> >> >> >>>>> I have the following files:
>>> >> >> >>>>> etc/gbrowse2/GBrowse.conf
>>> >> >> >>>>> var/www/gbrowse2/databases where I have the yeast_chr1+2
>>> >> >> >>>>> folder
>>> >> >> >>>>> with
>>> >> >> >>>>> my own data files
>>> >> >> >>>>> usr/lib/cgi-bin/gb2
>>> >> >> >>>>> var/lib/gbrowse2/databases/yeast_chr1+2 with other files
>>> >> >> >>>>>
>>> >> >> >>>>> but still the url http://localhost/cgi-bin/gbrowse2/yeast
>>> >> >> >>>>> shows
>>> >> >> >>>>> the
>>> >> >> >>>>> following url was not found on the server
>>> >> >> >>>>>
>>> >> >> >>>>> where is the cgi-bin mentioned in the url located when it is
>>> >> >> >>>>> not
>>> >> >> >>>>> in
>>> >> >> >>>>> /var/www/
>>> >> >> >>>>>
>>> >> >> >>>>> On Wed, Sep 17, 2014 at 8:54 AM, umay kulsum
>>> >> >> >>>>> <[hidden email]>
>>> >> >> >>>>> wrote:
>>> >> >> >>>>>> Hi
>>> >> >> >>>>>> I have installed GBrowse using the command in ubuntu 14.04
>>> >> >> >>>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>>> >> >> >>>>>> but when I point my browser to
>>> >> >> >>>>>> http://localhost/cgi-bin/gbrowse2/yeast, it shows the
>>> >> >> >>>>>> following
>>> >> >> >>>>>> url
>>> >> >> >>>>>> is
>>> >> >> >>>>>> not found on this server..
>>> >> >> >>>>>> where is the cgi-bin mentioned in the url located when it is
>>> >> >> >>>>>> not
>>> >> >> >>>>>> in
>>> >> >> >>>>>> /var/www/
>>> >> >> >>>>>>
>>> >> >> >>>>>>> On Tue, Sep 16, 2014 at 2:28 AM, Scott Cain
>>> >> >> >>>>>>> <[hidden email]>
>>> >> >> >>>>>>> wrote:
>>> >> >> >>>>>>> Hi Umay,
>>> >> >> >>>>>>>
>>> >> >> >>>>>>> Can you please tell us what you done and where you think the
>>> >> >> >>>>>>> process
>>> >> >> >>>>>>> has failed?  For instance, what do you see when you go to
>>> >> >> >>>>>>> the
>>> >> >> >>>>>>> built in
>>> >> >> >>>>>>> sample yeast data set?
>>> >> >> >>>>>>>
>>> >> >> >>>>>>> Scott
>>> >> >> >>>>>>>
>>> >> >> >>>>>>> Sent from my iPhone
>>> >> >> >>>>>>>
>>> >> >> >>>>>>>> On Sep 11, 2014, at 11:41 PM, umay kulsum
>>> >> >> >>>>>>>> <[hidden email]>
>>> >> >> >>>>>>>> wrote:
>>> >> >> >>>>>>>>
>>> >> >> >>>>>>>> I have been trying to install and invoke GBrowse since a
>>> >> >> >>>>>>>> month
>>> >> >> >>>>>>>> but to
>>> >> >> >>>>>>>> no result....
>>> >> >> >>>>>>>> can someone help me regarding the installation process.
>>> >> >> >>>>>>>>
>>> >> >> >>>>>>>>
>>> >> >> >>>>>>>>
>>> >> >> >>>>>>>>
>>> >> >> >>>>>>>>
>>> >> >> >>>>>>>> ------------------------------------------------------------------------------
>>> >> >> >>>>>>>> Want excitement?
>>> >> >> >>>>>>>> Manually upgrade your production database.
>>> >> >> >>>>>>>> When you want reliability, choose Perforce
>>> >> >> >>>>>>>> Perforce version control. Predictably reliable.
>>> >> >> >>>>>>>>
>>> >> >> >>>>>>>>
>>> >> >> >>>>>>>>
>>> >> >> >>>>>>>>
>>> >> >> >>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
>>> >> >> >>>>>>>> _______________________________________________
>>> >> >> >>>>>>>> Gmod-gbrowse mailing list
>>> >> >> >>>>>>>> [hidden email]
>>> >> >> >>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>> >> >> >>>>
>>> >> >> >>>>
>>> >> >> >>>>
>>> >> >> >>>>
>>> >> >> >>>> --
>>> >> >> >>>>
>>> >> >> >>>>
>>> >> >> >>>>
>>> >> >> >>>> ------------------------------------------------------------------------
>>> >> >> >>>> Scott Cain, Ph. D.                                   scott at
>>> >> >> >>>> scottcain dot
>>> >> >> >>>> net
>>> >> >> >>>> GMOD Coordinator (http://gmod.org/)
>>> >> >> >>>> 216-392-3087
>>> >> >> >>>> Ontario Institute for Cancer Research
>>> >> >
>>> >> >
>>> >> >
>>> >> >
>>> >> > --
>>> >> >
>>> >> > ------------------------------------------------------------------------
>>> >> > Scott Cain, Ph. D.                                   scott at
>>> >> > scottcain
>>> >> > dot
>>> >> > net
>>> >> > GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> >> > Ontario Institute for Cancer Research
>>> >
>>> >
>>> >
>>> >
>>> > --
>>> > ------------------------------------------------------------------------
>>> > Scott Cain, Ph. D.                                   scott at scottcain
>>> > dot
>>> > net
>>> > GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> > Ontario Institute for Cancer Research
>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot
>> net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research

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Re: help regarding gbrowse

Scott Cain
Hi Umay,

That message at the top of the screenshot you sent is the full error message.  The first line of it has the source of the problem.  It can't open the file at /var/lib/gbrowse2/databases/1......  Does that directory exist and does the webserver have permission to open it?  Probably the best thing to do is to change ownership of that directory to the user that runs the webserver:

  sudo chown -R www-data:www-data /var/lib/gbrowse2/databases/*

If you're making frequent edits in the databases directories (like when you're doing the tutorial), you can just make the directory you're working on world writeable, so that the webserver and you can both write files in the directory without sudo.  Of course, this is considerably less secure:

  sudo chmod -R a+w /var/lib/gbrowse2/databases/nameofdatabase

Scott


On Tue, Sep 23, 2014 at 11:52 PM, umay kulsum <[hidden email]> wrote:
hi Scott

I have created a script gbtry.php which is as follows:

<?php
$ourFileName = "/etc/gbrowse2/gbrowse.conf/".10190714.".conf";
$ourFileHandle = fopen($ourFileName, 'w') or die("can't open file");
$p="[GENERAL]
description   = motifs of ".21105857."protein
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
               -dir    '/var/www/html/gbrowse2/databases/10190714'


plugins = BatchDumper FastaDumper
gbrowse root = gbrowse
stylesheet   = gbrowse.css
buttons      = images/buttons
js           = js
tmpimages    = tmp
region segment = 500
initial landmark = \".21105857.\"
balloon tips    = 1
drag and drop = 1
cache time    = 1
link          = AUTO
image widths  = 450 640 800 1024
hilite fill    = beige
hilite outline = red
default width = 800
default features = \".21105857.\"
max segment     = 500
default segment = 50
zoom levels    = 50 100 200 1000 2000 5000 10000 20000 40000 100000
200000 500000 1000000
show sources   = 1
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
key bgcolor      = beige
examples =\".21105857.\"
automatic classes = \".21105857.\"


[protein]
feature      = protein
glyph        = so_transcript
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise
height       = 6
description  = 1
balloon hover width = 350
balloon hover = sub { my  = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
     <tr><th rowspan="5" align=\"left\"><br>
     This protein brought to you by <a
href=\"http://www.expasy.ch\">EXPASY</a>.</th>
         <th bgcolor=\"cyan\">Gene </th>
     </tr>
      <tr align='left'><th><a
href=\"/cgi-bin/gbrowse_details/motif?name=\">See protein
details</a></th></tr>
     <tr align='left'><th><a
href=\"<a href="http://www.ncbi.nlm.nih.gov/protein/\" target="_blank">http://www.ncbi.nlm.nih.gov/protein/\".21105857."">Go to
NCBI</a></th></tr>
      </table>

key          = protein
[pattern]
feature      = pattern
glyph        = so_transcript
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise
height       = 6
description  = 1
balloon hover width = 350
balloon hover = sub { my  = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
      <tr><th rowspan="5" align=\"left\"><br>
      This protein brought to you by <a
href=\"http://www.expasy.ch\">EXPASY</a>.</th>
         <th bgcolor=\"cyan\">Gene </th>
      </tr>
      <tr align='left'><th><a
href=\"/cgi-bin/gbrowse_details/motif?name=\">See gene
details</a></th></tr>
     <tr align='left'><th><a
href=\"<a href="http://en.wikipedia.org/wiki/Special:Search?search=\" target="_blank">http://en.wikipedia.org/wiki/Special:Search?search=\">Ask
Wikipedia about </a></th></tr>
      <tr align='left'><th><a
href=\"<a href="http://www.google.com/search?q=\" target="_blank">http://www.google.com/search?q=\">Ask Google about
</a></th></tr>
      </table>

key           = pattern



[profile]
feature      = profile
glyph        = so_transcript
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise
height       = 6
description  = 0
balloon hover width = 350
balloon hover = sub { my  = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
      <tr><th rowspan="5" align=\"left\"><br>
      This protein brought to you by <a
href=\"http://www.expasy.ch\">EXPASY</a>.</th>
          <th bgcolor=\"cyan\">Gene </th>
     </tr>
      <tr align='left'><th><a
href=\"<a href="http://en.wikipedia.org/wiki/Special:Search?search=/\" target="_blank">http://en.wikipedia.org/wiki/Special:Search?search=/\">Ask
Wikipedia about </a></th></tr>
     <tr align='left'><th><a
href=\"<a href="http://www.google.com/search?q=\" target="_blank">http://www.google.com/search?q=\">Ask Google about
</a></th></tr>
     </table>
key          = profile";
fwrite($ourFileHandle, $p);

$url="http://localhost/cgi-bin/gb2/gbrowse/".10190714;
echo "<br><iframe src =".$url." width="1000" height="700" >
</iframe>";}
?>



but when I point my browser to http://localhost/cgi-bin/gb2/gbrowse/10190714

I get the attached snapshot

On Wed, Sep 24, 2014 at 9:05 AM, umay kulsum <[hidden email]> wrote:
> Hi
>
> The error log shows:
> [cgi:error] [pid 17807] [client 127.0.0.1:34119] AH01215: STACK:
> /usr/lib/cgi-bin/gb2/gbrowse:55
>
> yes I added the entry to /etc/gbrowse/GBrowse.conf
>
> On Tue, Sep 23, 2014 at 6:52 PM, Scott Cain <[hidden email]> wrote:
>> Hi Umay,
>>
>> I'm glad you've gotten it working.
>>
>> What you're describing with asking for one configuration and getting another
>> is what happens when there is a problem with the configuration that you
>> want.  I don't see anything obvious with the configuration you pasted into
>> the email, but my eyes aren't as good a configuration parser as GBrowse.  A
>> few questions:
>>
>> Do you see anything in the apache error log that indicates that there is a
>> problem?
>>
>> Did you add an entry for the new configuration file to
>> /etc/gbrowse/GBrowse.conf?
>>
>> Scott
>>
>>
>> On Mon, Sep 22, 2014 at 11:35 PM, umay kulsum <[hidden email]> wrote:
>>>
>>> Hi
>>>
>>> Thank you scott....got GBrowse installed with git clone...
>>> example database of yeast is also working properly...
>>>
>>> but now I have created my own conf file as 114635370.conf in
>>> etc/gbrowse2/gbrowse.conf folder but when I run
>>> http://localhost/cgi-bin/gb2/gbrowse/114635370 it gives the result of
>>> yeast but not my own file
>>> why is it so and what can I do for that??
>>>
>>>
>>> my conf file is as follows:
>>>
>>> [GENERAL]
>>> description   = motifs of 114635370protein
>>> db_adaptor    = Bio::DB::SeqFeature::Store
>>> db_args       = -adaptor memory
>>>                -dir    '/var/www/html/gbrowse2/databases/1/1/4/114635370/'
>>>
>>>
>>> plugins = BatchDumper FastaDumper
>>> gbrowse root = gbrowse
>>> stylesheet   = gbrowse.css
>>> buttons      = images/buttons
>>> js           = js
>>> tmpimages    = tmp
>>> region segment = 500
>>> initial landmark = 114635370
>>> balloon tips    = 1
>>> drag and drop = 1
>>> cache time    = 1
>>> link          = AUTO
>>> image widths  = 450 640 800 1024
>>> hilite fill    = beige
>>> hilite outline = red
>>> default width = 800
>>> default features = 114635370
>>> max segment     = 500
>>> default segment = 50
>>> zoom levels    = 50 100 200 1000 2000 5000 10000 20000 40000 100000
>>> 200000 500000 1000000
>>> show sources   = 1
>>> overview bgcolor = lightgrey
>>> detailed bgcolor = lightgoldenrodyellow
>>> key bgcolor      = beige
>>> examples = 114635370
>>> automatic classes = 114635370
>>>
>>>
>>> [protein]
>>> feature      = protein
>>> glyph        = so_transcript
>>> bgcolor      = yellow
>>> forwardcolor = yellow
>>> reversecolor = turquoise
>>> height       = 6
>>> description  = 1
>>> balloon hover width = 350
>>> balloon hover = sub { my  = shift; return join ' ',->notes }
>>> balloon click width = 450
>>> balloon click = <table>
>>>      <tr><th rowspan="5" align="left"><br>
>>>      This protein brought to you by <a
>>> href="http://www.expasy.ch">EXPASY</a>.</th>
>>>          <th bgcolor="cyan">Gene </th>
>>>      </tr>
>>>       <tr align='left'><th><a
>>> href="/cgi-bin/gbrowse_details/motif?name=">See protein
>>> details</a></th></tr>
>>>      <tr align='left'><th><a
>>> href="http://www.ncbi.nlm.nih.gov/protein/114635370">Go to
>>> NCBI</a></th></tr>
>>>       </table>
>>>
>>> key          = protein
>>> [pattern]
>>> feature      = pattern
>>> glyph        = so_transcript
>>> bgcolor      = yellow
>>> forwardcolor = yellow
>>> reversecolor = turquoise
>>> height       = 6
>>> description  = 1
>>> balloon hover width = 350
>>> balloon hover = sub { my  = shift; return join ' ',->notes }
>>> balloon click width = 450
>>> balloon click = <table>
>>>       <tr><th rowspan="5" align="left"><br>
>>>       This protein brought to you by <a
>>> href="http://www.expasy.ch">EXPASY</a>.</th>
>>>          <th bgcolor="cyan">Gene </th>
>>>       </tr>
>>>       <tr align='left'><th><a
>>> href="/cgi-bin/gbrowse_details/motif?name=">See gene
>>> details</a></th></tr>
>>>      <tr align='left'><th><a
>>> href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
>>> Wikipedia about </a></th></tr>
>>>       <tr align='left'><th><a
>>> href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
>>>       </table>
>>>
>>> key           = pattern
>>>
>>>
>>>
>>> [profile]
>>> feature      = profile
>>> glyph        = so_transcript
>>> bgcolor      = yellow
>>> forwardcolor = yellow
>>> reversecolor = turquoise
>>> height       = 6
>>> description  = 0
>>> balloon hover width = 350
>>> balloon hover = sub { my  = shift; return join ' ',->notes }
>>> balloon click width = 450
>>> balloon click = <table>
>>>       <tr><th rowspan="5" align="left"><br>
>>>       This protein brought to you by <a
>>> href="http://www.expasy.ch">EXPASY</a>.</th>
>>>           <th bgcolor="cyan">Gene </th>
>>>      </tr>
>>>       <tr align='left'><th><a
>>> href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
>>> Wikipedia about </a></th></tr>
>>>      <tr align='left'><th><a
>>> href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
>>>      </table>
>>> key          = profile
>>>
>>> On Mon, Sep 22, 2014 at 5:36 PM, Scott Cain <[hidden email]> wrote:
>>> > Hi Umay,
>>> >
>>> > I don't really know what the problem is--my guess is that there is a
>>> > network
>>> > problem.  Can you try from a different network?  Can you clone other
>>> > things
>>> > from git but just not GBrowse (I would find that pretty strange if it
>>> > were
>>> > the case)?  Also, in case there is a problem with any of the software
>>> > packages you are using, you should probably run
>>> >
>>> >   sudo apt-get update
>>> >   sudo apt-get upgrade
>>> >
>>> > to make sure your system is up to date.
>>> >
>>> > Scott
>>> >
>>> >
>>> > On Mon, Sep 22, 2014 at 4:17 AM, umay kulsum <[hidden email]>
>>> > wrote:
>>> >>
>>> >> Hi
>>> >>
>>> >> when I do
>>> >> git clone https://github.com/GMOD/GBrowse.git
>>> >>
>>> >> I get the following error:
>>> >>
>>> >> Cloning into 'GBrowse'...
>>> >> fatal: unable to access 'https://github.com/GMOD/GBrowse.git/':
>>> >> gnutls_handshake() failed: A TLS packet with unexpected length was
>>> >> received.
>>> >>
>>> >> On Thu, Sep 18, 2014 at 7:37 PM, Scott Cain <[hidden email]>
>>> >> wrote:
>>> >> > Hi Umay,
>>> >> >
>>> >> > I suspect you are using Ubuntu 14.04 (you may have already told me
>>> >> > that--I
>>> >> > don't remember).  While working recently on some minor bug fixes for
>>> >> > GBrowse, we discovered that when Ubuntu 14.04 was released, they
>>> >> > dramatically rearranged the file structure for system files, which
>>> >> > broke
>>> >> > the
>>> >> > GBrowse installer.  The easiest way to install GBrowse correctly at
>>> >> > the
>>> >> > moment is to get a GitHub checkout of the current source and install
>>> >> > that
>>> >> > way.  It's fairly straight forward; this is what you do:
>>> >> >
>>> >> > git clone https://github.com/GMOD/GBrowse.git
>>> >> > cd GBrowse
>>> >> > perl Build.PL  #accepting the defaults should be fine
>>> >> > ./Build
>>> >> > ./Build test
>>> >> > sudo ./Build install
>>> >> >
>>> >> > After doing that you should be able to go to
>>> >> > http://localhost/gbrowse2
>>> >> > though the links for sample data sets are written assuming you have
>>> >> > fastcgi
>>> >> > installed (which is a good idea to use, because it makes things
>>> >> > faster),
>>> >> > but
>>> >> > if you don't have fastcgi, you should still be able to go to
>>> >> > http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset.
>>> >> > If
>>> >> > that
>>> >> > works, you should be able to proceed with the tutorial as well.
>>> >> >
>>> >> > On Thu, Sep 18, 2014 at 2:15 AM, umay kulsum <[hidden email]>
>>> >> > wrote:
>>> >> >>
>>> >> >> whenever we write localhost it looks for files in /var/www/html
>>> >> >> so I think its looking for /cgi-bin/gb2/gbrowse/yeast in /var/www
>>> >> >>
>>> >> >> On Thu, Sep 18, 2014 at 11:25 AM, umay kulsum
>>> >> >> <[hidden email]>
>>> >> >> wrote:
>>> >> >> > The apache error log shows :
>>> >> >> >
>>> >> >> > [Thu Sep 18 09:03:14.584273 2014] [core:notice] [pid 10766]
>>> >> >> > AH00094:
>>> >> >> > Command line: '/usr/sbin/apache2'
>>> >> >> >
>>> >> >> >
>>> >> >> > This is the last comment in /var/log/apache2/error.log...... it
>>> >> >> > shows
>>> >> >> > nothing regarding the files not found
>>> >> >> >
>>> >> >> >
>>> >> >> > In the access.log file the last comment is :
>>> >> >> >
>>> >> >> >
>>> >> >> > 127.0.0.1 - - [18/Sep/2014:11:13:58 +0530] "GET
>>> >> >> > /cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513 "-" "Mozilla/5.0
>>> >> >> > (X11;
>>> >> >> > Ubuntu; Linux x86_64; rv:28.0) Gecko/20100101 Firefox/28.0"
>>> >> >> >
>>> >> >> > On Thu, Sep 18, 2014 at 10:34 AM, Scott Cain <[hidden email]>
>>> >> >> > wrote:
>>> >> >> >> Hi Umay,
>>> >> >> >>
>>> >> >> >> What does it say in the apache error log?  If you're getting a
>>> >> >> >> message
>>> >> >> >> about a file not being found, it will record where it was looking
>>> >> >> >> for the
>>> >> >> >> file. The error log is in /var/log/apache2. The most recent
>>> >> >> >> message
>>> >> >> >> is at
>>> >> >> >> the end of the file.
>>> >> >> >>
>>> >> >> >> Scott
>>> >> >> >>
>>> >> >> >>
>>> >> >> >> Sent from my iPhone
>>> >> >> >>
>>> >> >> >>> On Sep 17, 2014, at 11:03 PM, umay kulsum
>>> >> >> >>> <[hidden email]>
>>> >> >> >>> wrote:
>>> >> >> >>>
>>> >> >> >>> hi
>>> >> >> >>> I have tried http://localhost/cgi-bin/gb2/gbrowse/yeast also but
>>> >> >> >>> again
>>> >> >> >>> its the same the requested url is not found on the server...
>>> >> >> >>> what should I do??
>>> >> >> >>> where am I going wrong??
>>> >> >> >>> can you please tell me how can I start from scratch that is
>>> >> >> >>> uninstall
>>> >> >> >>> and then reinstall....
>>> >> >> >>>
>>> >> >> >>>> On Wed, Sep 17, 2014 at 7:47 PM, Scott Cain
>>> >> >> >>>> <[hidden email]>
>>> >> >> >>>> wrote:
>>> >> >> >>>> Umay,
>>> >> >> >>>>
>>> >> >> >>>> Please "reply-all" so that your replies stay on the GBrowse
>>> >> >> >>>> mailing
>>> >> >> >>>> list.
>>> >> >> >>>>
>>> >> >> >>>> A few things:
>>> >> >> >>>>
>>> >> >> >>>> The url you are using is not correct; it should be
>>> >> >> >>>> http://localhost/cgi-bin/gb2/gbrowse/yeast.  This is linked to
>>> >> >> >>>> from
>>> >> >> >>>> http://localhost/gbrowse2/
>>> >> >> >>>>
>>> >> >> >>>> I don't know why you have two yeast_chr1+2 directories, but
>>> >> >> >>>> only
>>> >> >> >>>> one
>>> >> >> >>>> of them
>>> >> >> >>>> will work.  The typical configuration would be for the one in
>>> >> >> >>>> /var/lib/gbrowse2/databases to work.
>>> >> >> >>>>
>>> >> >> >>>> The cgi-bin directory is not in the /var/www directory when
>>> >> >> >>>> apache
>>> >> >> >>>> is
>>> >> >> >>>> typically configured for ubuntu; it's in /usr/lib/cgi-bin, as
>>> >> >> >>>> it
>>> >> >> >>>> is
>>> >> >> >>>> in your
>>> >> >> >>>> case.
>>> >> >> >>>>
>>> >> >> >>>> Scott
>>> >> >> >>>>
>>> >> >> >>>>
>>> >> >> >>>>> On Wed, Sep 17, 2014 at 4:15 AM, umay kulsum
>>> >> >> >>>>> <[hidden email]>
>>> >> >> >>>>> wrote:
>>> >> >> >>>>>
>>> >> >> >>>>> I have installed GBrowse using the command in ubuntu 14.04
>>> >> >> >>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>>> >> >> >>>>>
>>> >> >> >>>>> I have the following files:
>>> >> >> >>>>> etc/gbrowse2/GBrowse.conf
>>> >> >> >>>>> var/www/gbrowse2/databases where I have the yeast_chr1+2
>>> >> >> >>>>> folder
>>> >> >> >>>>> with
>>> >> >> >>>>> my own data files
>>> >> >> >>>>> usr/lib/cgi-bin/gb2
>>> >> >> >>>>> var/lib/gbrowse2/databases/yeast_chr1+2 with other files
>>> >> >> >>>>>
>>> >> >> >>>>> but still the url http://localhost/cgi-bin/gbrowse2/yeast
>>> >> >> >>>>> shows
>>> >> >> >>>>> the
>>> >> >> >>>>> following url was not found on the server
>>> >> >> >>>>>
>>> >> >> >>>>> where is the cgi-bin mentioned in the url located when it is
>>> >> >> >>>>> not
>>> >> >> >>>>> in
>>> >> >> >>>>> /var/www/
>>> >> >> >>>>>
>>> >> >> >>>>> On Wed, Sep 17, 2014 at 8:54 AM, umay kulsum
>>> >> >> >>>>> <[hidden email]>
>>> >> >> >>>>> wrote:
>>> >> >> >>>>>> Hi
>>> >> >> >>>>>> I have installed GBrowse using the command in ubuntu 14.04
>>> >> >> >>>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>>> >> >> >>>>>> but when I point my browser to
>>> >> >> >>>>>> http://localhost/cgi-bin/gbrowse2/yeast, it shows the
>>> >> >> >>>>>> following
>>> >> >> >>>>>> url
>>> >> >> >>>>>> is
>>> >> >> >>>>>> not found on this server..
>>> >> >> >>>>>> where is the cgi-bin mentioned in the url located when it is
>>> >> >> >>>>>> not
>>> >> >> >>>>>> in
>>> >> >> >>>>>> /var/www/
>>> >> >> >>>>>>
>>> >> >> >>>>>>> On Tue, Sep 16, 2014 at 2:28 AM, Scott Cain
>>> >> >> >>>>>>> <[hidden email]>
>>> >> >> >>>>>>> wrote:
>>> >> >> >>>>>>> Hi Umay,
>>> >> >> >>>>>>>
>>> >> >> >>>>>>> Can you please tell us what you done and where you think the
>>> >> >> >>>>>>> process
>>> >> >> >>>>>>> has failed?  For instance, what do you see when you go to
>>> >> >> >>>>>>> the
>>> >> >> >>>>>>> built in
>>> >> >> >>>>>>> sample yeast data set?
>>> >> >> >>>>>>>
>>> >> >> >>>>>>> Scott
>>> >> >> >>>>>>>
>>> >> >> >>>>>>> Sent from my iPhone
>>> >> >> >>>>>>>
>>> >> >> >>>>>>>> On Sep 11, 2014, at 11:41 PM, umay kulsum
>>> >> >> >>>>>>>> <[hidden email]>
>>> >> >> >>>>>>>> wrote:
>>> >> >> >>>>>>>>
>>> >> >> >>>>>>>> I have been trying to install and invoke GBrowse since a
>>> >> >> >>>>>>>> month
>>> >> >> >>>>>>>> but to
>>> >> >> >>>>>>>> no result....
>>> >> >> >>>>>>>> can someone help me regarding the installation process.
>>> >> >> >>>>>>>>
>>> >> >> >>>>>>>>
>>> >> >> >>>>>>>>
>>> >> >> >>>>>>>>
>>> >> >> >>>>>>>>
>>> >> >> >>>>>>>> ------------------------------------------------------------------------------
>>> >> >> >>>>>>>> Want excitement?
>>> >> >> >>>>>>>> Manually upgrade your production database.
>>> >> >> >>>>>>>> When you want reliability, choose Perforce
>>> >> >> >>>>>>>> Perforce version control. Predictably reliable.
>>> >> >> >>>>>>>>
>>> >> >> >>>>>>>>
>>> >> >> >>>>>>>>
>>> >> >> >>>>>>>>
>>> >> >> >>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
>>> >> >> >>>>>>>> _______________________________________________
>>> >> >> >>>>>>>> Gmod-gbrowse mailing list
>>> >> >> >>>>>>>> [hidden email]
>>> >> >> >>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>> >> >> >>>>
>>> >> >> >>>>
>>> >> >> >>>>
>>> >> >> >>>>
>>> >> >> >>>> --
>>> >> >> >>>>
>>> >> >> >>>>
>>> >> >> >>>>
>>> >> >> >>>> ------------------------------------------------------------------------
>>> >> >> >>>> Scott Cain, Ph. D.                                   scott at
>>> >> >> >>>> scottcain dot
>>> >> >> >>>> net
>>> >> >> >>>> GMOD Coordinator (http://gmod.org/)
>>> >> >> >>>> <a href="tel:216-392-3087" value="+12163923087">216-392-3087
>>> >> >> >>>> Ontario Institute for Cancer Research
>>> >> >
>>> >> >
>>> >> >
>>> >> >
>>> >> > --
>>> >> >
>>> >> > ------------------------------------------------------------------------
>>> >> > Scott Cain, Ph. D.                                   scott at
>>> >> > scottcain
>>> >> > dot
>>> >> > net
>>> >> > GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
>>> >> > Ontario Institute for Cancer Research
>>> >
>>> >
>>> >
>>> >
>>> > --
>>> > ------------------------------------------------------------------------
>>> > Scott Cain, Ph. D.                                   scott at scottcain
>>> > dot
>>> > net
>>> > GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
>>> > Ontario Institute for Cancer Research
>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot
>> net
>> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
>> Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: help regarding gbrowse

umay kulsum
Hi Scott,

I have done as you directed. The error message is no more there but
not getting the tracks.
screenshot is attached.



On Wed, Sep 24, 2014 at 8:33 PM, Scott Cain <[hidden email]> wrote:

> Hi Umay,
>
> That message at the top of the screenshot you sent is the full error
> message.  The first line of it has the source of the problem.  It can't open
> the file at /var/lib/gbrowse2/databases/1......  Does that directory exist
> and does the webserver have permission to open it?  Probably the best thing
> to do is to change ownership of that directory to the user that runs the
> webserver:
>
>   sudo chown -R www-data:www-data /var/lib/gbrowse2/databases/*
>
> If you're making frequent edits in the databases directories (like when
> you're doing the tutorial), you can just make the directory you're working
> on world writeable, so that the webserver and you can both write files in
> the directory without sudo.  Of course, this is considerably less secure:
>
>   sudo chmod -R a+w /var/lib/gbrowse2/databases/nameofdatabase
>
> Scott
>
>
> On Tue, Sep 23, 2014 at 11:52 PM, umay kulsum <[hidden email]> wrote:
>>
>> hi Scott
>>
>> I have created a script gbtry.php which is as follows:
>>
>> <?php
>> $ourFileName = "/etc/gbrowse2/gbrowse.conf/".10190714.".conf";
>> $ourFileHandle = fopen($ourFileName, 'w') or die("can't open file");
>> $p="[GENERAL]
>> description   = motifs of ".21105857."protein
>> db_adaptor    = Bio::DB::SeqFeature::Store
>> db_args       = -adaptor memory
>>                -dir    '/var/www/html/gbrowse2/databases/10190714'
>>
>>
>> plugins = BatchDumper FastaDumper
>> gbrowse root = gbrowse
>> stylesheet   = gbrowse.css
>> buttons      = images/buttons
>> js           = js
>> tmpimages    = tmp
>> region segment = 500
>> initial landmark = \".21105857.\"
>> balloon tips    = 1
>> drag and drop = 1
>> cache time    = 1
>> link          = AUTO
>> image widths  = 450 640 800 1024
>> hilite fill    = beige
>> hilite outline = red
>> default width = 800
>> default features = \".21105857.\"
>> max segment     = 500
>> default segment = 50
>> zoom levels    = 50 100 200 1000 2000 5000 10000 20000 40000 100000
>> 200000 500000 1000000
>> show sources   = 1
>> overview bgcolor = lightgrey
>> detailed bgcolor = lightgoldenrodyellow
>> key bgcolor      = beige
>> examples =\".21105857.\"
>> automatic classes = \".21105857.\"
>>
>>
>> [protein]
>> feature      = protein
>> glyph        = so_transcript
>> bgcolor      = yellow
>> forwardcolor = yellow
>> reversecolor = turquoise
>> height       = 6
>> description  = 1
>> balloon hover width = 350
>> balloon hover = sub { my  = shift; return join ' ',->notes }
>> balloon click width = 450
>> balloon click = <table>
>>      <tr><th rowspan="5" align=\"left\"><br>
>>      This protein brought to you by <a
>> href=\"http://www.expasy.ch\">EXPASY</a>.</th>
>>          <th bgcolor=\"cyan\">Gene </th>
>>      </tr>
>>       <tr align='left'><th><a
>> href=\"/cgi-bin/gbrowse_details/motif?name=\">See protein
>> details</a></th></tr>
>>      <tr align='left'><th><a
>> href=\"http://www.ncbi.nlm.nih.gov/protein/\".21105857."">Go to
>> NCBI</a></th></tr>
>>       </table>
>>
>> key          = protein
>> [pattern]
>> feature      = pattern
>> glyph        = so_transcript
>> bgcolor      = yellow
>> forwardcolor = yellow
>> reversecolor = turquoise
>> height       = 6
>> description  = 1
>> balloon hover width = 350
>> balloon hover = sub { my  = shift; return join ' ',->notes }
>> balloon click width = 450
>> balloon click = <table>
>>       <tr><th rowspan="5" align=\"left\"><br>
>>       This protein brought to you by <a
>> href=\"http://www.expasy.ch\">EXPASY</a>.</th>
>>          <th bgcolor=\"cyan\">Gene </th>
>>       </tr>
>>       <tr align='left'><th><a
>> href=\"/cgi-bin/gbrowse_details/motif?name=\">See gene
>> details</a></th></tr>
>>      <tr align='left'><th><a
>> href=\"http://en.wikipedia.org/wiki/Special:Search?search=\">Ask
>> Wikipedia about </a></th></tr>
>>       <tr align='left'><th><a
>> href=\"http://www.google.com/search?q=\">Ask Google about
>> </a></th></tr>
>>       </table>
>>
>> key           = pattern
>>
>>
>>
>> [profile]
>> feature      = profile
>> glyph        = so_transcript
>> bgcolor      = yellow
>> forwardcolor = yellow
>> reversecolor = turquoise
>> height       = 6
>> description  = 0
>> balloon hover width = 350
>> balloon hover = sub { my  = shift; return join ' ',->notes }
>> balloon click width = 450
>> balloon click = <table>
>>       <tr><th rowspan="5" align=\"left\"><br>
>>       This protein brought to you by <a
>> href=\"http://www.expasy.ch\">EXPASY</a>.</th>
>>           <th bgcolor=\"cyan\">Gene </th>
>>      </tr>
>>       <tr align='left'><th><a
>> href=\"http://en.wikipedia.org/wiki/Special:Search?search=/\">Ask
>> Wikipedia about </a></th></tr>
>>      <tr align='left'><th><a
>> href=\"http://www.google.com/search?q=\">Ask Google about
>> </a></th></tr>
>>      </table>
>> key          = profile";
>> fwrite($ourFileHandle, $p);
>>
>> $url="http://localhost/cgi-bin/gb2/gbrowse/".10190714;
>> echo "<br><iframe src =".$url." width="1000" height="700" >
>> </iframe>";}
>> ?>
>>
>>
>>
>> but when I point my browser to
>> http://localhost/cgi-bin/gb2/gbrowse/10190714
>>
>> I get the attached snapshot
>>
>> On Wed, Sep 24, 2014 at 9:05 AM, umay kulsum <[hidden email]>
>> wrote:
>> > Hi
>> >
>> > The error log shows:
>> > [cgi:error] [pid 17807] [client 127.0.0.1:34119] AH01215: STACK:
>> > /usr/lib/cgi-bin/gb2/gbrowse:55
>> >
>> > yes I added the entry to /etc/gbrowse/GBrowse.conf
>> >
>> > On Tue, Sep 23, 2014 at 6:52 PM, Scott Cain <[hidden email]> wrote:
>> >> Hi Umay,
>> >>
>> >> I'm glad you've gotten it working.
>> >>
>> >> What you're describing with asking for one configuration and getting
>> >> another
>> >> is what happens when there is a problem with the configuration that you
>> >> want.  I don't see anything obvious with the configuration you pasted
>> >> into
>> >> the email, but my eyes aren't as good a configuration parser as
>> >> GBrowse.  A
>> >> few questions:
>> >>
>> >> Do you see anything in the apache error log that indicates that there
>> >> is a
>> >> problem?
>> >>
>> >> Did you add an entry for the new configuration file to
>> >> /etc/gbrowse/GBrowse.conf?
>> >>
>> >> Scott
>> >>
>> >>
>> >> On Mon, Sep 22, 2014 at 11:35 PM, umay kulsum <[hidden email]>
>> >> wrote:
>> >>>
>> >>> Hi
>> >>>
>> >>> Thank you scott....got GBrowse installed with git clone...
>> >>> example database of yeast is also working properly...
>> >>>
>> >>> but now I have created my own conf file as 114635370.conf in
>> >>> etc/gbrowse2/gbrowse.conf folder but when I run
>> >>> http://localhost/cgi-bin/gb2/gbrowse/114635370 it gives the result of
>> >>> yeast but not my own file
>> >>> why is it so and what can I do for that??
>> >>>
>> >>>
>> >>> my conf file is as follows:
>> >>>
>> >>> [GENERAL]
>> >>> description   = motifs of 114635370protein
>> >>> db_adaptor    = Bio::DB::SeqFeature::Store
>> >>> db_args       = -adaptor memory
>> >>>                -dir
>> >>> '/var/www/html/gbrowse2/databases/1/1/4/114635370/'
>> >>>
>> >>>
>> >>> plugins = BatchDumper FastaDumper
>> >>> gbrowse root = gbrowse
>> >>> stylesheet   = gbrowse.css
>> >>> buttons      = images/buttons
>> >>> js           = js
>> >>> tmpimages    = tmp
>> >>> region segment = 500
>> >>> initial landmark = 114635370
>> >>> balloon tips    = 1
>> >>> drag and drop = 1
>> >>> cache time    = 1
>> >>> link          = AUTO
>> >>> image widths  = 450 640 800 1024
>> >>> hilite fill    = beige
>> >>> hilite outline = red
>> >>> default width = 800
>> >>> default features = 114635370
>> >>> max segment     = 500
>> >>> default segment = 50
>> >>> zoom levels    = 50 100 200 1000 2000 5000 10000 20000 40000 100000
>> >>> 200000 500000 1000000
>> >>> show sources   = 1
>> >>> overview bgcolor = lightgrey
>> >>> detailed bgcolor = lightgoldenrodyellow
>> >>> key bgcolor      = beige
>> >>> examples = 114635370
>> >>> automatic classes = 114635370
>> >>>
>> >>>
>> >>> [protein]
>> >>> feature      = protein
>> >>> glyph        = so_transcript
>> >>> bgcolor      = yellow
>> >>> forwardcolor = yellow
>> >>> reversecolor = turquoise
>> >>> height       = 6
>> >>> description  = 1
>> >>> balloon hover width = 350
>> >>> balloon hover = sub { my  = shift; return join ' ',->notes }
>> >>> balloon click width = 450
>> >>> balloon click = <table>
>> >>>      <tr><th rowspan="5" align="left"><br>
>> >>>      This protein brought to you by <a
>> >>> href="http://www.expasy.ch">EXPASY</a>.</th>
>> >>>          <th bgcolor="cyan">Gene </th>
>> >>>      </tr>
>> >>>       <tr align='left'><th><a
>> >>> href="/cgi-bin/gbrowse_details/motif?name=">See protein
>> >>> details</a></th></tr>
>> >>>      <tr align='left'><th><a
>> >>> href="http://www.ncbi.nlm.nih.gov/protein/114635370">Go to
>> >>> NCBI</a></th></tr>
>> >>>       </table>
>> >>>
>> >>> key          = protein
>> >>> [pattern]
>> >>> feature      = pattern
>> >>> glyph        = so_transcript
>> >>> bgcolor      = yellow
>> >>> forwardcolor = yellow
>> >>> reversecolor = turquoise
>> >>> height       = 6
>> >>> description  = 1
>> >>> balloon hover width = 350
>> >>> balloon hover = sub { my  = shift; return join ' ',->notes }
>> >>> balloon click width = 450
>> >>> balloon click = <table>
>> >>>       <tr><th rowspan="5" align="left"><br>
>> >>>       This protein brought to you by <a
>> >>> href="http://www.expasy.ch">EXPASY</a>.</th>
>> >>>          <th bgcolor="cyan">Gene </th>
>> >>>       </tr>
>> >>>       <tr align='left'><th><a
>> >>> href="/cgi-bin/gbrowse_details/motif?name=">See gene
>> >>> details</a></th></tr>
>> >>>      <tr align='left'><th><a
>> >>> href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
>> >>> Wikipedia about </a></th></tr>
>> >>>       <tr align='left'><th><a
>> >>> href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
>> >>>       </table>
>> >>>
>> >>> key           = pattern
>> >>>
>> >>>
>> >>>
>> >>> [profile]
>> >>> feature      = profile
>> >>> glyph        = so_transcript
>> >>> bgcolor      = yellow
>> >>> forwardcolor = yellow
>> >>> reversecolor = turquoise
>> >>> height       = 6
>> >>> description  = 0
>> >>> balloon hover width = 350
>> >>> balloon hover = sub { my  = shift; return join ' ',->notes }
>> >>> balloon click width = 450
>> >>> balloon click = <table>
>> >>>       <tr><th rowspan="5" align="left"><br>
>> >>>       This protein brought to you by <a
>> >>> href="http://www.expasy.ch">EXPASY</a>.</th>
>> >>>           <th bgcolor="cyan">Gene </th>
>> >>>      </tr>
>> >>>       <tr align='left'><th><a
>> >>> href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
>> >>> Wikipedia about </a></th></tr>
>> >>>      <tr align='left'><th><a
>> >>> href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
>> >>>      </table>
>> >>> key          = profile
>> >>>
>> >>> On Mon, Sep 22, 2014 at 5:36 PM, Scott Cain <[hidden email]>
>> >>> wrote:
>> >>> > Hi Umay,
>> >>> >
>> >>> > I don't really know what the problem is--my guess is that there is a
>> >>> > network
>> >>> > problem.  Can you try from a different network?  Can you clone other
>> >>> > things
>> >>> > from git but just not GBrowse (I would find that pretty strange if
>> >>> > it
>> >>> > were
>> >>> > the case)?  Also, in case there is a problem with any of the
>> >>> > software
>> >>> > packages you are using, you should probably run
>> >>> >
>> >>> >   sudo apt-get update
>> >>> >   sudo apt-get upgrade
>> >>> >
>> >>> > to make sure your system is up to date.
>> >>> >
>> >>> > Scott
>> >>> >
>> >>> >
>> >>> > On Mon, Sep 22, 2014 at 4:17 AM, umay kulsum <[hidden email]>
>> >>> > wrote:
>> >>> >>
>> >>> >> Hi
>> >>> >>
>> >>> >> when I do
>> >>> >> git clone https://github.com/GMOD/GBrowse.git
>> >>> >>
>> >>> >> I get the following error:
>> >>> >>
>> >>> >> Cloning into 'GBrowse'...
>> >>> >> fatal: unable to access 'https://github.com/GMOD/GBrowse.git/':
>> >>> >> gnutls_handshake() failed: A TLS packet with unexpected length was
>> >>> >> received.
>> >>> >>
>> >>> >> On Thu, Sep 18, 2014 at 7:37 PM, Scott Cain <[hidden email]>
>> >>> >> wrote:
>> >>> >> > Hi Umay,
>> >>> >> >
>> >>> >> > I suspect you are using Ubuntu 14.04 (you may have already told
>> >>> >> > me
>> >>> >> > that--I
>> >>> >> > don't remember).  While working recently on some minor bug fixes
>> >>> >> > for
>> >>> >> > GBrowse, we discovered that when Ubuntu 14.04 was released, they
>> >>> >> > dramatically rearranged the file structure for system files,
>> >>> >> > which
>> >>> >> > broke
>> >>> >> > the
>> >>> >> > GBrowse installer.  The easiest way to install GBrowse correctly
>> >>> >> > at
>> >>> >> > the
>> >>> >> > moment is to get a GitHub checkout of the current source and
>> >>> >> > install
>> >>> >> > that
>> >>> >> > way.  It's fairly straight forward; this is what you do:
>> >>> >> >
>> >>> >> > git clone https://github.com/GMOD/GBrowse.git
>> >>> >> > cd GBrowse
>> >>> >> > perl Build.PL  #accepting the defaults should be fine
>> >>> >> > ./Build
>> >>> >> > ./Build test
>> >>> >> > sudo ./Build install
>> >>> >> >
>> >>> >> > After doing that you should be able to go to
>> >>> >> > http://localhost/gbrowse2
>> >>> >> > though the links for sample data sets are written assuming you
>> >>> >> > have
>> >>> >> > fastcgi
>> >>> >> > installed (which is a good idea to use, because it makes things
>> >>> >> > faster),
>> >>> >> > but
>> >>> >> > if you don't have fastcgi, you should still be able to go to
>> >>> >> > http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample
>> >>> >> > dataset.
>> >>> >> > If
>> >>> >> > that
>> >>> >> > works, you should be able to proceed with the tutorial as well.
>> >>> >> >
>> >>> >> > On Thu, Sep 18, 2014 at 2:15 AM, umay kulsum
>> >>> >> > <[hidden email]>
>> >>> >> > wrote:
>> >>> >> >>
>> >>> >> >> whenever we write localhost it looks for files in /var/www/html
>> >>> >> >> so I think its looking for /cgi-bin/gb2/gbrowse/yeast in
>> >>> >> >> /var/www
>> >>> >> >>
>> >>> >> >> On Thu, Sep 18, 2014 at 11:25 AM, umay kulsum
>> >>> >> >> <[hidden email]>
>> >>> >> >> wrote:
>> >>> >> >> > The apache error log shows :
>> >>> >> >> >
>> >>> >> >> > [Thu Sep 18 09:03:14.584273 2014] [core:notice] [pid 10766]
>> >>> >> >> > AH00094:
>> >>> >> >> > Command line: '/usr/sbin/apache2'
>> >>> >> >> >
>> >>> >> >> >
>> >>> >> >> > This is the last comment in /var/log/apache2/error.log......
>> >>> >> >> > it
>> >>> >> >> > shows
>> >>> >> >> > nothing regarding the files not found
>> >>> >> >> >
>> >>> >> >> >
>> >>> >> >> > In the access.log file the last comment is :
>> >>> >> >> >
>> >>> >> >> >
>> >>> >> >> > 127.0.0.1 - - [18/Sep/2014:11:13:58 +0530] "GET
>> >>> >> >> > /cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513 "-" "Mozilla/5.0
>> >>> >> >> > (X11;
>> >>> >> >> > Ubuntu; Linux x86_64; rv:28.0) Gecko/20100101 Firefox/28.0"
>> >>> >> >> >
>> >>> >> >> > On Thu, Sep 18, 2014 at 10:34 AM, Scott Cain
>> >>> >> >> > <[hidden email]>
>> >>> >> >> > wrote:
>> >>> >> >> >> Hi Umay,
>> >>> >> >> >>
>> >>> >> >> >> What does it say in the apache error log?  If you're getting
>> >>> >> >> >> a
>> >>> >> >> >> message
>> >>> >> >> >> about a file not being found, it will record where it was
>> >>> >> >> >> looking
>> >>> >> >> >> for the
>> >>> >> >> >> file. The error log is in /var/log/apache2. The most recent
>> >>> >> >> >> message
>> >>> >> >> >> is at
>> >>> >> >> >> the end of the file.
>> >>> >> >> >>
>> >>> >> >> >> Scott
>> >>> >> >> >>
>> >>> >> >> >>
>> >>> >> >> >> Sent from my iPhone
>> >>> >> >> >>
>> >>> >> >> >>> On Sep 17, 2014, at 11:03 PM, umay kulsum
>> >>> >> >> >>> <[hidden email]>
>> >>> >> >> >>> wrote:
>> >>> >> >> >>>
>> >>> >> >> >>> hi
>> >>> >> >> >>> I have tried http://localhost/cgi-bin/gb2/gbrowse/yeast also
>> >>> >> >> >>> but
>> >>> >> >> >>> again
>> >>> >> >> >>> its the same the requested url is not found on the server...
>> >>> >> >> >>> what should I do??
>> >>> >> >> >>> where am I going wrong??
>> >>> >> >> >>> can you please tell me how can I start from scratch that is
>> >>> >> >> >>> uninstall
>> >>> >> >> >>> and then reinstall....
>> >>> >> >> >>>
>> >>> >> >> >>>> On Wed, Sep 17, 2014 at 7:47 PM, Scott Cain
>> >>> >> >> >>>> <[hidden email]>
>> >>> >> >> >>>> wrote:
>> >>> >> >> >>>> Umay,
>> >>> >> >> >>>>
>> >>> >> >> >>>> Please "reply-all" so that your replies stay on the GBrowse
>> >>> >> >> >>>> mailing
>> >>> >> >> >>>> list.
>> >>> >> >> >>>>
>> >>> >> >> >>>> A few things:
>> >>> >> >> >>>>
>> >>> >> >> >>>> The url you are using is not correct; it should be
>> >>> >> >> >>>> http://localhost/cgi-bin/gb2/gbrowse/yeast.  This is linked
>> >>> >> >> >>>> to
>> >>> >> >> >>>> from
>> >>> >> >> >>>> http://localhost/gbrowse2/
>> >>> >> >> >>>>
>> >>> >> >> >>>> I don't know why you have two yeast_chr1+2 directories, but
>> >>> >> >> >>>> only
>> >>> >> >> >>>> one
>> >>> >> >> >>>> of them
>> >>> >> >> >>>> will work.  The typical configuration would be for the one
>> >>> >> >> >>>> in
>> >>> >> >> >>>> /var/lib/gbrowse2/databases to work.
>> >>> >> >> >>>>
>> >>> >> >> >>>> The cgi-bin directory is not in the /var/www directory when
>> >>> >> >> >>>> apache
>> >>> >> >> >>>> is
>> >>> >> >> >>>> typically configured for ubuntu; it's in /usr/lib/cgi-bin,
>> >>> >> >> >>>> as
>> >>> >> >> >>>> it
>> >>> >> >> >>>> is
>> >>> >> >> >>>> in your
>> >>> >> >> >>>> case.
>> >>> >> >> >>>>
>> >>> >> >> >>>> Scott
>> >>> >> >> >>>>
>> >>> >> >> >>>>
>> >>> >> >> >>>>> On Wed, Sep 17, 2014 at 4:15 AM, umay kulsum
>> >>> >> >> >>>>> <[hidden email]>
>> >>> >> >> >>>>> wrote:
>> >>> >> >> >>>>>
>> >>> >> >> >>>>> I have installed GBrowse using the command in ubuntu 14.04
>> >>> >> >> >>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>> >>> >> >> >>>>>
>> >>> >> >> >>>>> I have the following files:
>> >>> >> >> >>>>> etc/gbrowse2/GBrowse.conf
>> >>> >> >> >>>>> var/www/gbrowse2/databases where I have the yeast_chr1+2
>> >>> >> >> >>>>> folder
>> >>> >> >> >>>>> with
>> >>> >> >> >>>>> my own data files
>> >>> >> >> >>>>> usr/lib/cgi-bin/gb2
>> >>> >> >> >>>>> var/lib/gbrowse2/databases/yeast_chr1+2 with other files
>> >>> >> >> >>>>>
>> >>> >> >> >>>>> but still the url http://localhost/cgi-bin/gbrowse2/yeast
>> >>> >> >> >>>>> shows
>> >>> >> >> >>>>> the
>> >>> >> >> >>>>> following url was not found on the server
>> >>> >> >> >>>>>
>> >>> >> >> >>>>> where is the cgi-bin mentioned in the url located when it
>> >>> >> >> >>>>> is
>> >>> >> >> >>>>> not
>> >>> >> >> >>>>> in
>> >>> >> >> >>>>> /var/www/
>> >>> >> >> >>>>>
>> >>> >> >> >>>>> On Wed, Sep 17, 2014 at 8:54 AM, umay kulsum
>> >>> >> >> >>>>> <[hidden email]>
>> >>> >> >> >>>>> wrote:
>> >>> >> >> >>>>>> Hi
>> >>> >> >> >>>>>> I have installed GBrowse using the command in ubuntu
>> >>> >> >> >>>>>> 14.04
>> >>> >> >> >>>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>> >>> >> >> >>>>>> but when I point my browser to
>> >>> >> >> >>>>>> http://localhost/cgi-bin/gbrowse2/yeast, it shows the
>> >>> >> >> >>>>>> following
>> >>> >> >> >>>>>> url
>> >>> >> >> >>>>>> is
>> >>> >> >> >>>>>> not found on this server..
>> >>> >> >> >>>>>> where is the cgi-bin mentioned in the url located when it
>> >>> >> >> >>>>>> is
>> >>> >> >> >>>>>> not
>> >>> >> >> >>>>>> in
>> >>> >> >> >>>>>> /var/www/
>> >>> >> >> >>>>>>
>> >>> >> >> >>>>>>> On Tue, Sep 16, 2014 at 2:28 AM, Scott Cain
>> >>> >> >> >>>>>>> <[hidden email]>
>> >>> >> >> >>>>>>> wrote:
>> >>> >> >> >>>>>>> Hi Umay,
>> >>> >> >> >>>>>>>
>> >>> >> >> >>>>>>> Can you please tell us what you done and where you think
>> >>> >> >> >>>>>>> the
>> >>> >> >> >>>>>>> process
>> >>> >> >> >>>>>>> has failed?  For instance, what do you see when you go
>> >>> >> >> >>>>>>> to
>> >>> >> >> >>>>>>> the
>> >>> >> >> >>>>>>> built in
>> >>> >> >> >>>>>>> sample yeast data set?
>> >>> >> >> >>>>>>>
>> >>> >> >> >>>>>>> Scott
>> >>> >> >> >>>>>>>
>> >>> >> >> >>>>>>> Sent from my iPhone
>> >>> >> >> >>>>>>>
>> >>> >> >> >>>>>>>> On Sep 11, 2014, at 11:41 PM, umay kulsum
>> >>> >> >> >>>>>>>> <[hidden email]>
>> >>> >> >> >>>>>>>> wrote:
>> >>> >> >> >>>>>>>>
>> >>> >> >> >>>>>>>> I have been trying to install and invoke GBrowse since
>> >>> >> >> >>>>>>>> a
>> >>> >> >> >>>>>>>> month
>> >>> >> >> >>>>>>>> but to
>> >>> >> >> >>>>>>>> no result....
>> >>> >> >> >>>>>>>> can someone help me regarding the installation process.
>> >>> >> >> >>>>>>>>
>> >>> >> >> >>>>>>>>
>> >>> >> >> >>>>>>>>
>> >>> >> >> >>>>>>>>
>> >>> >> >> >>>>>>>>
>> >>> >> >> >>>>>>>>
>> >>> >> >> >>>>>>>> ------------------------------------------------------------------------------
>> >>> >> >> >>>>>>>> Want excitement?
>> >>> >> >> >>>>>>>> Manually upgrade your production database.
>> >>> >> >> >>>>>>>> When you want reliability, choose Perforce
>> >>> >> >> >>>>>>>> Perforce version control. Predictably reliable.
>> >>> >> >> >>>>>>>>
>> >>> >> >> >>>>>>>>
>> >>> >> >> >>>>>>>>
>> >>> >> >> >>>>>>>>
>> >>> >> >> >>>>>>>>
>> >>> >> >> >>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
>> >>> >> >> >>>>>>>> _______________________________________________
>> >>> >> >> >>>>>>>> Gmod-gbrowse mailing list
>> >>> >> >> >>>>>>>> [hidden email]
>> >>> >> >> >>>>>>>>
>> >>> >> >> >>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >>> >> >> >>>>
>> >>> >> >> >>>>
>> >>> >> >> >>>>
>> >>> >> >> >>>>
>> >>> >> >> >>>> --
>> >>> >> >> >>>>
>> >>> >> >> >>>>
>> >>> >> >> >>>>
>> >>> >> >> >>>>
>> >>> >> >> >>>> ------------------------------------------------------------------------
>> >>> >> >> >>>> Scott Cain, Ph. D.                                   scott
>> >>> >> >> >>>> at
>> >>> >> >> >>>> scottcain dot
>> >>> >> >> >>>> net
>> >>> >> >> >>>> GMOD Coordinator (http://gmod.org/)
>> >>> >> >> >>>> 216-392-3087
>> >>> >> >> >>>> Ontario Institute for Cancer Research
>> >>> >> >
>> >>> >> >
>> >>> >> >
>> >>> >> >
>> >>> >> > --
>> >>> >> >
>> >>> >> >
>> >>> >> > ------------------------------------------------------------------------
>> >>> >> > Scott Cain, Ph. D.                                   scott at
>> >>> >> > scottcain
>> >>> >> > dot
>> >>> >> > net
>> >>> >> > GMOD Coordinator (http://gmod.org/)
>> >>> >> > 216-392-3087
>> >>> >> > Ontario Institute for Cancer Research
>> >>> >
>> >>> >
>> >>> >
>> >>> >
>> >>> > --
>> >>> >
>> >>> > ------------------------------------------------------------------------
>> >>> > Scott Cain, Ph. D.                                   scott at
>> >>> > scottcain
>> >>> > dot
>> >>> > net
>> >>> > GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >>> > Ontario Institute for Cancer Research
>> >>
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> Scott Cain, Ph. D.                                   scott at scottcain
>> >> dot
>> >> net
>> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> Ontario Institute for Cancer Research
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research

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Re: help regarding gbrowse

umay kulsum
Hi Scott

I have done as you directed. The error message is no more there but
not getting the tracks.
screenshot is attached.
and the gff3 file is not being displayed when I open
/var/lib/gbrowse2/databases.
the gff3 file is also attached.

On Fri, Sep 26, 2014 at 8:35 AM, umay kulsum <[hidden email]> wrote:

> Hi Scott,
>
> I have done as you directed. The error message is no more there but
> not getting the tracks.
> screenshot is attached.
>
>
>
> On Wed, Sep 24, 2014 at 8:33 PM, Scott Cain <[hidden email]> wrote:
>> Hi Umay,
>>
>> That message at the top of the screenshot you sent is the full error
>> message.  The first line of it has the source of the problem.  It can't open
>> the file at /var/lib/gbrowse2/databases/1......  Does that directory exist
>> and does the webserver have permission to open it?  Probably the best thing
>> to do is to change ownership of that directory to the user that runs the
>> webserver:
>>
>>   sudo chown -R www-data:www-data /var/lib/gbrowse2/databases/*
>>
>> If you're making frequent edits in the databases directories (like when
>> you're doing the tutorial), you can just make the directory you're working
>> on world writeable, so that the webserver and you can both write files in
>> the directory without sudo.  Of course, this is considerably less secure:
>>
>>   sudo chmod -R a+w /var/lib/gbrowse2/databases/nameofdatabase
>>
>> Scott
>>
>>
>> On Tue, Sep 23, 2014 at 11:52 PM, umay kulsum <[hidden email]> wrote:
>>>
>>> hi Scott
>>>
>>> I have created a script gbtry.php which is as follows:
>>>
>>> <?php
>>> $ourFileName = "/etc/gbrowse2/gbrowse.conf/".10190714.".conf";
>>> $ourFileHandle = fopen($ourFileName, 'w') or die("can't open file");
>>> $p="[GENERAL]
>>> description   = motifs of ".21105857."protein
>>> db_adaptor    = Bio::DB::SeqFeature::Store
>>> db_args       = -adaptor memory
>>>                -dir    '/var/www/html/gbrowse2/databases/10190714'
>>>
>>>
>>> plugins = BatchDumper FastaDumper
>>> gbrowse root = gbrowse
>>> stylesheet   = gbrowse.css
>>> buttons      = images/buttons
>>> js           = js
>>> tmpimages    = tmp
>>> region segment = 500
>>> initial landmark = \".21105857.\"
>>> balloon tips    = 1
>>> drag and drop = 1
>>> cache time    = 1
>>> link          = AUTO
>>> image widths  = 450 640 800 1024
>>> hilite fill    = beige
>>> hilite outline = red
>>> default width = 800
>>> default features = \".21105857.\"
>>> max segment     = 500
>>> default segment = 50
>>> zoom levels    = 50 100 200 1000 2000 5000 10000 20000 40000 100000
>>> 200000 500000 1000000
>>> show sources   = 1
>>> overview bgcolor = lightgrey
>>> detailed bgcolor = lightgoldenrodyellow
>>> key bgcolor      = beige
>>> examples =\".21105857.\"
>>> automatic classes = \".21105857.\"
>>>
>>>
>>> [protein]
>>> feature      = protein
>>> glyph        = so_transcript
>>> bgcolor      = yellow
>>> forwardcolor = yellow
>>> reversecolor = turquoise
>>> height       = 6
>>> description  = 1
>>> balloon hover width = 350
>>> balloon hover = sub { my  = shift; return join ' ',->notes }
>>> balloon click width = 450
>>> balloon click = <table>
>>>      <tr><th rowspan="5" align=\"left\"><br>
>>>      This protein brought to you by <a
>>> href=\"http://www.expasy.ch\">EXPASY</a>.</th>
>>>          <th bgcolor=\"cyan\">Gene </th>
>>>      </tr>
>>>       <tr align='left'><th><a
>>> href=\"/cgi-bin/gbrowse_details/motif?name=\">See protein
>>> details</a></th></tr>
>>>      <tr align='left'><th><a
>>> href=\"http://www.ncbi.nlm.nih.gov/protein/\".21105857."">Go to
>>> NCBI</a></th></tr>
>>>       </table>
>>>
>>> key          = protein
>>> [pattern]
>>> feature      = pattern
>>> glyph        = so_transcript
>>> bgcolor      = yellow
>>> forwardcolor = yellow
>>> reversecolor = turquoise
>>> height       = 6
>>> description  = 1
>>> balloon hover width = 350
>>> balloon hover = sub { my  = shift; return join ' ',->notes }
>>> balloon click width = 450
>>> balloon click = <table>
>>>       <tr><th rowspan="5" align=\"left\"><br>
>>>       This protein brought to you by <a
>>> href=\"http://www.expasy.ch\">EXPASY</a>.</th>
>>>          <th bgcolor=\"cyan\">Gene </th>
>>>       </tr>
>>>       <tr align='left'><th><a
>>> href=\"/cgi-bin/gbrowse_details/motif?name=\">See gene
>>> details</a></th></tr>
>>>      <tr align='left'><th><a
>>> href=\"http://en.wikipedia.org/wiki/Special:Search?search=\">Ask
>>> Wikipedia about </a></th></tr>
>>>       <tr align='left'><th><a
>>> href=\"http://www.google.com/search?q=\">Ask Google about
>>> </a></th></tr>
>>>       </table>
>>>
>>> key           = pattern
>>>
>>>
>>>
>>> [profile]
>>> feature      = profile
>>> glyph        = so_transcript
>>> bgcolor      = yellow
>>> forwardcolor = yellow
>>> reversecolor = turquoise
>>> height       = 6
>>> description  = 0
>>> balloon hover width = 350
>>> balloon hover = sub { my  = shift; return join ' ',->notes }
>>> balloon click width = 450
>>> balloon click = <table>
>>>       <tr><th rowspan="5" align=\"left\"><br>
>>>       This protein brought to you by <a
>>> href=\"http://www.expasy.ch\">EXPASY</a>.</th>
>>>           <th bgcolor=\"cyan\">Gene </th>
>>>      </tr>
>>>       <tr align='left'><th><a
>>> href=\"http://en.wikipedia.org/wiki/Special:Search?search=/\">Ask
>>> Wikipedia about </a></th></tr>
>>>      <tr align='left'><th><a
>>> href=\"http://www.google.com/search?q=\">Ask Google about
>>> </a></th></tr>
>>>      </table>
>>> key          = profile";
>>> fwrite($ourFileHandle, $p);
>>>
>>> $url="http://localhost/cgi-bin/gb2/gbrowse/".10190714;
>>> echo "<br><iframe src =".$url." width="1000" height="700" >
>>> </iframe>";}
>>> ?>
>>>
>>>
>>>
>>> but when I point my browser to
>>> http://localhost/cgi-bin/gb2/gbrowse/10190714
>>>
>>> I get the attached snapshot
>>>
>>> On Wed, Sep 24, 2014 at 9:05 AM, umay kulsum <[hidden email]>
>>> wrote:
>>> > Hi
>>> >
>>> > The error log shows:
>>> > [cgi:error] [pid 17807] [client 127.0.0.1:34119] AH01215: STACK:
>>> > /usr/lib/cgi-bin/gb2/gbrowse:55
>>> >
>>> > yes I added the entry to /etc/gbrowse/GBrowse.conf
>>> >
>>> > On Tue, Sep 23, 2014 at 6:52 PM, Scott Cain <[hidden email]> wrote:
>>> >> Hi Umay,
>>> >>
>>> >> I'm glad you've gotten it working.
>>> >>
>>> >> What you're describing with asking for one configuration and getting
>>> >> another
>>> >> is what happens when there is a problem with the configuration that you
>>> >> want.  I don't see anything obvious with the configuration you pasted
>>> >> into
>>> >> the email, but my eyes aren't as good a configuration parser as
>>> >> GBrowse.  A
>>> >> few questions:
>>> >>
>>> >> Do you see anything in the apache error log that indicates that there
>>> >> is a
>>> >> problem?
>>> >>
>>> >> Did you add an entry for the new configuration file to
>>> >> /etc/gbrowse/GBrowse.conf?
>>> >>
>>> >> Scott
>>> >>
>>> >>
>>> >> On Mon, Sep 22, 2014 at 11:35 PM, umay kulsum <[hidden email]>
>>> >> wrote:
>>> >>>
>>> >>> Hi
>>> >>>
>>> >>> Thank you scott....got GBrowse installed with git clone...
>>> >>> example database of yeast is also working properly...
>>> >>>
>>> >>> but now I have created my own conf file as 114635370.conf in
>>> >>> etc/gbrowse2/gbrowse.conf folder but when I run
>>> >>> http://localhost/cgi-bin/gb2/gbrowse/114635370 it gives the result of
>>> >>> yeast but not my own file
>>> >>> why is it so and what can I do for that??
>>> >>>
>>> >>>
>>> >>> my conf file is as follows:
>>> >>>
>>> >>> [GENERAL]
>>> >>> description   = motifs of 114635370protein
>>> >>> db_adaptor    = Bio::DB::SeqFeature::Store
>>> >>> db_args       = -adaptor memory
>>> >>>                -dir
>>> >>> '/var/www/html/gbrowse2/databases/1/1/4/114635370/'
>>> >>>
>>> >>>
>>> >>> plugins = BatchDumper FastaDumper
>>> >>> gbrowse root = gbrowse
>>> >>> stylesheet   = gbrowse.css
>>> >>> buttons      = images/buttons
>>> >>> js           = js
>>> >>> tmpimages    = tmp
>>> >>> region segment = 500
>>> >>> initial landmark = 114635370
>>> >>> balloon tips    = 1
>>> >>> drag and drop = 1
>>> >>> cache time    = 1
>>> >>> link          = AUTO
>>> >>> image widths  = 450 640 800 1024
>>> >>> hilite fill    = beige
>>> >>> hilite outline = red
>>> >>> default width = 800
>>> >>> default features = 114635370
>>> >>> max segment     = 500
>>> >>> default segment = 50
>>> >>> zoom levels    = 50 100 200 1000 2000 5000 10000 20000 40000 100000
>>> >>> 200000 500000 1000000
>>> >>> show sources   = 1
>>> >>> overview bgcolor = lightgrey
>>> >>> detailed bgcolor = lightgoldenrodyellow
>>> >>> key bgcolor      = beige
>>> >>> examples = 114635370
>>> >>> automatic classes = 114635370
>>> >>>
>>> >>>
>>> >>> [protein]
>>> >>> feature      = protein
>>> >>> glyph        = so_transcript
>>> >>> bgcolor      = yellow
>>> >>> forwardcolor = yellow
>>> >>> reversecolor = turquoise
>>> >>> height       = 6
>>> >>> description  = 1
>>> >>> balloon hover width = 350
>>> >>> balloon hover = sub { my  = shift; return join ' ',->notes }
>>> >>> balloon click width = 450
>>> >>> balloon click = <table>
>>> >>>      <tr><th rowspan="5" align="left"><br>
>>> >>>      This protein brought to you by <a
>>> >>> href="http://www.expasy.ch">EXPASY</a>.</th>
>>> >>>          <th bgcolor="cyan">Gene </th>
>>> >>>      </tr>
>>> >>>       <tr align='left'><th><a
>>> >>> href="/cgi-bin/gbrowse_details/motif?name=">See protein
>>> >>> details</a></th></tr>
>>> >>>      <tr align='left'><th><a
>>> >>> href="http://www.ncbi.nlm.nih.gov/protein/114635370">Go to
>>> >>> NCBI</a></th></tr>
>>> >>>       </table>
>>> >>>
>>> >>> key          = protein
>>> >>> [pattern]
>>> >>> feature      = pattern
>>> >>> glyph        = so_transcript
>>> >>> bgcolor      = yellow
>>> >>> forwardcolor = yellow
>>> >>> reversecolor = turquoise
>>> >>> height       = 6
>>> >>> description  = 1
>>> >>> balloon hover width = 350
>>> >>> balloon hover = sub { my  = shift; return join ' ',->notes }
>>> >>> balloon click width = 450
>>> >>> balloon click = <table>
>>> >>>       <tr><th rowspan="5" align="left"><br>
>>> >>>       This protein brought to you by <a
>>> >>> href="http://www.expasy.ch">EXPASY</a>.</th>
>>> >>>          <th bgcolor="cyan">Gene </th>
>>> >>>       </tr>
>>> >>>       <tr align='left'><th><a
>>> >>> href="/cgi-bin/gbrowse_details/motif?name=">See gene
>>> >>> details</a></th></tr>
>>> >>>      <tr align='left'><th><a
>>> >>> href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
>>> >>> Wikipedia about </a></th></tr>
>>> >>>       <tr align='left'><th><a
>>> >>> href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
>>> >>>       </table>
>>> >>>
>>> >>> key           = pattern
>>> >>>
>>> >>>
>>> >>>
>>> >>> [profile]
>>> >>> feature      = profile
>>> >>> glyph        = so_transcript
>>> >>> bgcolor      = yellow
>>> >>> forwardcolor = yellow
>>> >>> reversecolor = turquoise
>>> >>> height       = 6
>>> >>> description  = 0
>>> >>> balloon hover width = 350
>>> >>> balloon hover = sub { my  = shift; return join ' ',->notes }
>>> >>> balloon click width = 450
>>> >>> balloon click = <table>
>>> >>>       <tr><th rowspan="5" align="left"><br>
>>> >>>       This protein brought to you by <a
>>> >>> href="http://www.expasy.ch">EXPASY</a>.</th>
>>> >>>           <th bgcolor="cyan">Gene </th>
>>> >>>      </tr>
>>> >>>       <tr align='left'><th><a
>>> >>> href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
>>> >>> Wikipedia about </a></th></tr>
>>> >>>      <tr align='left'><th><a
>>> >>> href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
>>> >>>      </table>
>>> >>> key          = profile
>>> >>>
>>> >>> On Mon, Sep 22, 2014 at 5:36 PM, Scott Cain <[hidden email]>
>>> >>> wrote:
>>> >>> > Hi Umay,
>>> >>> >
>>> >>> > I don't really know what the problem is--my guess is that there is a
>>> >>> > network
>>> >>> > problem.  Can you try from a different network?  Can you clone other
>>> >>> > things
>>> >>> > from git but just not GBrowse (I would find that pretty strange if
>>> >>> > it
>>> >>> > were
>>> >>> > the case)?  Also, in case there is a problem with any of the
>>> >>> > software
>>> >>> > packages you are using, you should probably run
>>> >>> >
>>> >>> >   sudo apt-get update
>>> >>> >   sudo apt-get upgrade
>>> >>> >
>>> >>> > to make sure your system is up to date.
>>> >>> >
>>> >>> > Scott
>>> >>> >
>>> >>> >
>>> >>> > On Mon, Sep 22, 2014 at 4:17 AM, umay kulsum <[hidden email]>
>>> >>> > wrote:
>>> >>> >>
>>> >>> >> Hi
>>> >>> >>
>>> >>> >> when I do
>>> >>> >> git clone https://github.com/GMOD/GBrowse.git
>>> >>> >>
>>> >>> >> I get the following error:
>>> >>> >>
>>> >>> >> Cloning into 'GBrowse'...
>>> >>> >> fatal: unable to access 'https://github.com/GMOD/GBrowse.git/':
>>> >>> >> gnutls_handshake() failed: A TLS packet with unexpected length was
>>> >>> >> received.
>>> >>> >>
>>> >>> >> On Thu, Sep 18, 2014 at 7:37 PM, Scott Cain <[hidden email]>
>>> >>> >> wrote:
>>> >>> >> > Hi Umay,
>>> >>> >> >
>>> >>> >> > I suspect you are using Ubuntu 14.04 (you may have already told
>>> >>> >> > me
>>> >>> >> > that--I
>>> >>> >> > don't remember).  While working recently on some minor bug fixes
>>> >>> >> > for
>>> >>> >> > GBrowse, we discovered that when Ubuntu 14.04 was released, they
>>> >>> >> > dramatically rearranged the file structure for system files,
>>> >>> >> > which
>>> >>> >> > broke
>>> >>> >> > the
>>> >>> >> > GBrowse installer.  The easiest way to install GBrowse correctly
>>> >>> >> > at
>>> >>> >> > the
>>> >>> >> > moment is to get a GitHub checkout of the current source and
>>> >>> >> > install
>>> >>> >> > that
>>> >>> >> > way.  It's fairly straight forward; this is what you do:
>>> >>> >> >
>>> >>> >> > git clone https://github.com/GMOD/GBrowse.git
>>> >>> >> > cd GBrowse
>>> >>> >> > perl Build.PL  #accepting the defaults should be fine
>>> >>> >> > ./Build
>>> >>> >> > ./Build test
>>> >>> >> > sudo ./Build install
>>> >>> >> >
>>> >>> >> > After doing that you should be able to go to
>>> >>> >> > http://localhost/gbrowse2
>>> >>> >> > though the links for sample data sets are written assuming you
>>> >>> >> > have
>>> >>> >> > fastcgi
>>> >>> >> > installed (which is a good idea to use, because it makes things
>>> >>> >> > faster),
>>> >>> >> > but
>>> >>> >> > if you don't have fastcgi, you should still be able to go to
>>> >>> >> > http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample
>>> >>> >> > dataset.
>>> >>> >> > If
>>> >>> >> > that
>>> >>> >> > works, you should be able to proceed with the tutorial as well.
>>> >>> >> >
>>> >>> >> > On Thu, Sep 18, 2014 at 2:15 AM, umay kulsum
>>> >>> >> > <[hidden email]>
>>> >>> >> > wrote:
>>> >>> >> >>
>>> >>> >> >> whenever we write localhost it looks for files in /var/www/html
>>> >>> >> >> so I think its looking for /cgi-bin/gb2/gbrowse/yeast in
>>> >>> >> >> /var/www
>>> >>> >> >>
>>> >>> >> >> On Thu, Sep 18, 2014 at 11:25 AM, umay kulsum
>>> >>> >> >> <[hidden email]>
>>> >>> >> >> wrote:
>>> >>> >> >> > The apache error log shows :
>>> >>> >> >> >
>>> >>> >> >> > [Thu Sep 18 09:03:14.584273 2014] [core:notice] [pid 10766]
>>> >>> >> >> > AH00094:
>>> >>> >> >> > Command line: '/usr/sbin/apache2'
>>> >>> >> >> >
>>> >>> >> >> >
>>> >>> >> >> > This is the last comment in /var/log/apache2/error.log......
>>> >>> >> >> > it
>>> >>> >> >> > shows
>>> >>> >> >> > nothing regarding the files not found
>>> >>> >> >> >
>>> >>> >> >> >
>>> >>> >> >> > In the access.log file the last comment is :
>>> >>> >> >> >
>>> >>> >> >> >
>>> >>> >> >> > 127.0.0.1 - - [18/Sep/2014:11:13:58 +0530] "GET
>>> >>> >> >> > /cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513 "-" "Mozilla/5.0
>>> >>> >> >> > (X11;
>>> >>> >> >> > Ubuntu; Linux x86_64; rv:28.0) Gecko/20100101 Firefox/28.0"
>>> >>> >> >> >
>>> >>> >> >> > On Thu, Sep 18, 2014 at 10:34 AM, Scott Cain
>>> >>> >> >> > <[hidden email]>
>>> >>> >> >> > wrote:
>>> >>> >> >> >> Hi Umay,
>>> >>> >> >> >>
>>> >>> >> >> >> What does it say in the apache error log?  If you're getting
>>> >>> >> >> >> a
>>> >>> >> >> >> message
>>> >>> >> >> >> about a file not being found, it will record where it was
>>> >>> >> >> >> looking
>>> >>> >> >> >> for the
>>> >>> >> >> >> file. The error log is in /var/log/apache2. The most recent
>>> >>> >> >> >> message
>>> >>> >> >> >> is at
>>> >>> >> >> >> the end of the file.
>>> >>> >> >> >>
>>> >>> >> >> >> Scott
>>> >>> >> >> >>
>>> >>> >> >> >>
>>> >>> >> >> >> Sent from my iPhone
>>> >>> >> >> >>
>>> >>> >> >> >>> On Sep 17, 2014, at 11:03 PM, umay kulsum
>>> >>> >> >> >>> <[hidden email]>
>>> >>> >> >> >>> wrote:
>>> >>> >> >> >>>
>>> >>> >> >> >>> hi
>>> >>> >> >> >>> I have tried http://localhost/cgi-bin/gb2/gbrowse/yeast also
>>> >>> >> >> >>> but
>>> >>> >> >> >>> again
>>> >>> >> >> >>> its the same the requested url is not found on the server...
>>> >>> >> >> >>> what should I do??
>>> >>> >> >> >>> where am I going wrong??
>>> >>> >> >> >>> can you please tell me how can I start from scratch that is
>>> >>> >> >> >>> uninstall
>>> >>> >> >> >>> and then reinstall....
>>> >>> >> >> >>>
>>> >>> >> >> >>>> On Wed, Sep 17, 2014 at 7:47 PM, Scott Cain
>>> >>> >> >> >>>> <[hidden email]>
>>> >>> >> >> >>>> wrote:
>>> >>> >> >> >>>> Umay,
>>> >>> >> >> >>>>
>>> >>> >> >> >>>> Please "reply-all" so that your replies stay on the GBrowse
>>> >>> >> >> >>>> mailing
>>> >>> >> >> >>>> list.
>>> >>> >> >> >>>>
>>> >>> >> >> >>>> A few things:
>>> >>> >> >> >>>>
>>> >>> >> >> >>>> The url you are using is not correct; it should be
>>> >>> >> >> >>>> http://localhost/cgi-bin/gb2/gbrowse/yeast.  This is linked
>>> >>> >> >> >>>> to
>>> >>> >> >> >>>> from
>>> >>> >> >> >>>> http://localhost/gbrowse2/
>>> >>> >> >> >>>>
>>> >>> >> >> >>>> I don't know why you have two yeast_chr1+2 directories, but
>>> >>> >> >> >>>> only
>>> >>> >> >> >>>> one
>>> >>> >> >> >>>> of them
>>> >>> >> >> >>>> will work.  The typical configuration would be for the one
>>> >>> >> >> >>>> in
>>> >>> >> >> >>>> /var/lib/gbrowse2/databases to work.
>>> >>> >> >> >>>>
>>> >>> >> >> >>>> The cgi-bin directory is not in the /var/www directory when
>>> >>> >> >> >>>> apache
>>> >>> >> >> >>>> is
>>> >>> >> >> >>>> typically configured for ubuntu; it's in /usr/lib/cgi-bin,
>>> >>> >> >> >>>> as
>>> >>> >> >> >>>> it
>>> >>> >> >> >>>> is
>>> >>> >> >> >>>> in your
>>> >>> >> >> >>>> case.
>>> >>> >> >> >>>>
>>> >>> >> >> >>>> Scott
>>> >>> >> >> >>>>
>>> >>> >> >> >>>>
>>> >>> >> >> >>>>> On Wed, Sep 17, 2014 at 4:15 AM, umay kulsum
>>> >>> >> >> >>>>> <[hidden email]>
>>> >>> >> >> >>>>> wrote:
>>> >>> >> >> >>>>>
>>> >>> >> >> >>>>> I have installed GBrowse using the command in ubuntu 14.04
>>> >>> >> >> >>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>>> >>> >> >> >>>>>
>>> >>> >> >> >>>>> I have the following files:
>>> >>> >> >> >>>>> etc/gbrowse2/GBrowse.conf
>>> >>> >> >> >>>>> var/www/gbrowse2/databases where I have the yeast_chr1+2
>>> >>> >> >> >>>>> folder
>>> >>> >> >> >>>>> with
>>> >>> >> >> >>>>> my own data files
>>> >>> >> >> >>>>> usr/lib/cgi-bin/gb2
>>> >>> >> >> >>>>> var/lib/gbrowse2/databases/yeast_chr1+2 with other files
>>> >>> >> >> >>>>>
>>> >>> >> >> >>>>> but still the url http://localhost/cgi-bin/gbrowse2/yeast
>>> >>> >> >> >>>>> shows
>>> >>> >> >> >>>>> the
>>> >>> >> >> >>>>> following url was not found on the server
>>> >>> >> >> >>>>>
>>> >>> >> >> >>>>> where is the cgi-bin mentioned in the url located when it
>>> >>> >> >> >>>>> is
>>> >>> >> >> >>>>> not
>>> >>> >> >> >>>>> in
>>> >>> >> >> >>>>> /var/www/
>>> >>> >> >> >>>>>
>>> >>> >> >> >>>>> On Wed, Sep 17, 2014 at 8:54 AM, umay kulsum
>>> >>> >> >> >>>>> <[hidden email]>
>>> >>> >> >> >>>>> wrote:
>>> >>> >> >> >>>>>> Hi
>>> >>> >> >> >>>>>> I have installed GBrowse using the command in ubuntu
>>> >>> >> >> >>>>>> 14.04
>>> >>> >> >> >>>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>>> >>> >> >> >>>>>> but when I point my browser to
>>> >>> >> >> >>>>>> http://localhost/cgi-bin/gbrowse2/yeast, it shows the
>>> >>> >> >> >>>>>> following
>>> >>> >> >> >>>>>> url
>>> >>> >> >> >>>>>> is
>>> >>> >> >> >>>>>> not found on this server..
>>> >>> >> >> >>>>>> where is the cgi-bin mentioned in the url located when it
>>> >>> >> >> >>>>>> is
>>> >>> >> >> >>>>>> not
>>> >>> >> >> >>>>>> in
>>> >>> >> >> >>>>>> /var/www/
>>> >>> >> >> >>>>>>
>>> >>> >> >> >>>>>>> On Tue, Sep 16, 2014 at 2:28 AM, Scott Cain
>>> >>> >> >> >>>>>>> <[hidden email]>
>>> >>> >> >> >>>>>>> wrote:
>>> >>> >> >> >>>>>>> Hi Umay,
>>> >>> >> >> >>>>>>>
>>> >>> >> >> >>>>>>> Can you please tell us what you done and where you think
>>> >>> >> >> >>>>>>> the
>>> >>> >> >> >>>>>>> process
>>> >>> >> >> >>>>>>> has failed?  For instance, what do you see when you go
>>> >>> >> >> >>>>>>> to
>>> >>> >> >> >>>>>>> the
>>> >>> >> >> >>>>>>> built in
>>> >>> >> >> >>>>>>> sample yeast data set?
>>> >>> >> >> >>>>>>>
>>> >>> >> >> >>>>>>> Scott
>>> >>> >> >> >>>>>>>
>>> >>> >> >> >>>>>>> Sent from my iPhone
>>> >>> >> >> >>>>>>>
>>> >>> >> >> >>>>>>>> On Sep 11, 2014, at 11:41 PM, umay kulsum
>>> >>> >> >> >>>>>>>> <[hidden email]>
>>> >>> >> >> >>>>>>>> wrote:
>>> >>> >> >> >>>>>>>>
>>> >>> >> >> >>>>>>>> I have been trying to install and invoke GBrowse since
>>> >>> >> >> >>>>>>>> a
>>> >>> >> >> >>>>>>>> month
>>> >>> >> >> >>>>>>>> but to
>>> >>> >> >> >>>>>>>> no result....
>>> >>> >> >> >>>>>>>> can someone help me regarding the installation process.
>>> >>> >> >> >>>>>>>>
>>> >>> >> >> >>>>>>>>
>>> >>> >> >> >>>>>>>>
>>> >>> >> >> >>>>>>>>
>>> >>> >> >> >>>>>>>>
>>> >>> >> >> >>>>>>>>
>>> >>> >> >> >>>>>>>> ------------------------------------------------------------------------------
>>> >>> >> >> >>>>>>>> Want excitement?
>>> >>> >> >> >>>>>>>> Manually upgrade your production database.
>>> >>> >> >> >>>>>>>> When you want reliability, choose Perforce
>>> >>> >> >> >>>>>>>> Perforce version control. Predictably reliable.
>>> >>> >> >> >>>>>>>>
>>> >>> >> >> >>>>>>>>
>>> >>> >> >> >>>>>>>>
>>> >>> >> >> >>>>>>>>
>>> >>> >> >> >>>>>>>>
>>> >>> >> >> >>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
>>> >>> >> >> >>>>>>>> _______________________________________________
>>> >>> >> >> >>>>>>>> Gmod-gbrowse mailing list
>>> >>> >> >> >>>>>>>> [hidden email]
>>> >>> >> >> >>>>>>>>
>>> >>> >> >> >>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>> >>> >> >> >>>>
>>> >>> >> >> >>>>
>>> >>> >> >> >>>>
>>> >>> >> >> >>>>
>>> >>> >> >> >>>> --
>>> >>> >> >> >>>>
>>> >>> >> >> >>>>
>>> >>> >> >> >>>>
>>> >>> >> >> >>>>
>>> >>> >> >> >>>> ------------------------------------------------------------------------
>>> >>> >> >> >>>> Scott Cain, Ph. D.                                   scott
>>> >>> >> >> >>>> at
>>> >>> >> >> >>>> scottcain dot
>>> >>> >> >> >>>> net
>>> >>> >> >> >>>> GMOD Coordinator (http://gmod.org/)
>>> >>> >> >> >>>> 216-392-3087
>>> >>> >> >> >>>> Ontario Institute for Cancer Research
>>> >>> >> >
>>> >>> >> >
>>> >>> >> >
>>> >>> >> >
>>> >>> >> > --
>>> >>> >> >
>>> >>> >> >
>>> >>> >> > ------------------------------------------------------------------------
>>> >>> >> > Scott Cain, Ph. D.                                   scott at
>>> >>> >> > scottcain
>>> >>> >> > dot
>>> >>> >> > net
>>> >>> >> > GMOD Coordinator (http://gmod.org/)
>>> >>> >> > 216-392-3087
>>> >>> >> > Ontario Institute for Cancer Research
>>> >>> >
>>> >>> >
>>> >>> >
>>> >>> >
>>> >>> > --
>>> >>> >
>>> >>> > ------------------------------------------------------------------------
>>> >>> > Scott Cain, Ph. D.                                   scott at
>>> >>> > scottcain
>>> >>> > dot
>>> >>> > net
>>> >>> > GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> >>> > Ontario Institute for Cancer Research
>>> >>
>>> >>
>>> >>
>>> >>
>>> >> --
>>> >>
>>> >> ------------------------------------------------------------------------
>>> >> Scott Cain, Ph. D.                                   scott at scottcain
>>> >> dot
>>> >> net
>>> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> >> Ontario Institute for Cancer Research
>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot
>> net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research

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Re: help regarding gbrowse

umay kulsum
Hi Scott

I have done as you directed. The error message is no more there but
not getting the tracks.
screenshot is attached.
and the gff3 file is not being displayed when I open
/var/lib/gbrowse2/databases.
the gff3 file is also attached.

The command chown -R www-data:www-data changes the gff3 file from
plain text to binary
The original gff3 is also attached

On Fri, Sep 26, 2014 at 9:17 AM, umay kulsum <[hidden email]> wrote:

> Hi Scott
>
> I have done as you directed. The error message is no more there but
> not getting the tracks.
> screenshot is attached.
> and the gff3 file is not being displayed when I open
> /var/lib/gbrowse2/databases.
> the gff3 file is also attached.
>
> On Fri, Sep 26, 2014 at 8:35 AM, umay kulsum <[hidden email]> wrote:
>> Hi Scott,
>>
>> I have done as you directed. The error message is no more there but
>> not getting the tracks.
>> screenshot is attached.
>>
>>
>>
>> On Wed, Sep 24, 2014 at 8:33 PM, Scott Cain <[hidden email]> wrote:
>>> Hi Umay,
>>>
>>> That message at the top of the screenshot you sent is the full error
>>> message.  The first line of it has the source of the problem.  It can't open
>>> the file at /var/lib/gbrowse2/databases/1......  Does that directory exist
>>> and does the webserver have permission to open it?  Probably the best thing
>>> to do is to change ownership of that directory to the user that runs the
>>> webserver:
>>>
>>>   sudo chown -R www-data:www-data /var/lib/gbrowse2/databases/*
>>>
>>> If you're making frequent edits in the databases directories (like when
>>> you're doing the tutorial), you can just make the directory you're working
>>> on world writeable, so that the webserver and you can both write files in
>>> the directory without sudo.  Of course, this is considerably less secure:
>>>
>>>   sudo chmod -R a+w /var/lib/gbrowse2/databases/nameofdatabase
>>>
>>> Scott
>>>
>>>
>>> On Tue, Sep 23, 2014 at 11:52 PM, umay kulsum <[hidden email]> wrote:
>>>>
>>>> hi Scott
>>>>
>>>> I have created a script gbtry.php which is as follows:
>>>>
>>>> <?php
>>>> $ourFileName = "/etc/gbrowse2/gbrowse.conf/".10190714.".conf";
>>>> $ourFileHandle = fopen($ourFileName, 'w') or die("can't open file");
>>>> $p="[GENERAL]
>>>> description   = motifs of ".21105857."protein
>>>> db_adaptor    = Bio::DB::SeqFeature::Store
>>>> db_args       = -adaptor memory
>>>>                -dir    '/var/www/html/gbrowse2/databases/10190714'
>>>>
>>>>
>>>> plugins = BatchDumper FastaDumper
>>>> gbrowse root = gbrowse
>>>> stylesheet   = gbrowse.css
>>>> buttons      = images/buttons
>>>> js           = js
>>>> tmpimages    = tmp
>>>> region segment = 500
>>>> initial landmark = \".21105857.\"
>>>> balloon tips    = 1
>>>> drag and drop = 1
>>>> cache time    = 1
>>>> link          = AUTO
>>>> image widths  = 450 640 800 1024
>>>> hilite fill    = beige
>>>> hilite outline = red
>>>> default width = 800
>>>> default features = \".21105857.\"
>>>> max segment     = 500
>>>> default segment = 50
>>>> zoom levels    = 50 100 200 1000 2000 5000 10000 20000 40000 100000
>>>> 200000 500000 1000000
>>>> show sources   = 1
>>>> overview bgcolor = lightgrey
>>>> detailed bgcolor = lightgoldenrodyellow
>>>> key bgcolor      = beige
>>>> examples =\".21105857.\"
>>>> automatic classes = \".21105857.\"
>>>>
>>>>
>>>> [protein]
>>>> feature      = protein
>>>> glyph        = so_transcript
>>>> bgcolor      = yellow
>>>> forwardcolor = yellow
>>>> reversecolor = turquoise
>>>> height       = 6
>>>> description  = 1
>>>> balloon hover width = 350
>>>> balloon hover = sub { my  = shift; return join ' ',->notes }
>>>> balloon click width = 450
>>>> balloon click = <table>
>>>>      <tr><th rowspan="5" align=\"left\"><br>
>>>>      This protein brought to you by <a
>>>> href=\"http://www.expasy.ch\">EXPASY</a>.</th>
>>>>          <th bgcolor=\"cyan\">Gene </th>
>>>>      </tr>
>>>>       <tr align='left'><th><a
>>>> href=\"/cgi-bin/gbrowse_details/motif?name=\">See protein
>>>> details</a></th></tr>
>>>>      <tr align='left'><th><a
>>>> href=\"http://www.ncbi.nlm.nih.gov/protein/\".21105857."">Go to
>>>> NCBI</a></th></tr>
>>>>       </table>
>>>>
>>>> key          = protein
>>>> [pattern]
>>>> feature      = pattern
>>>> glyph        = so_transcript
>>>> bgcolor      = yellow
>>>> forwardcolor = yellow
>>>> reversecolor = turquoise
>>>> height       = 6
>>>> description  = 1
>>>> balloon hover width = 350
>>>> balloon hover = sub { my  = shift; return join ' ',->notes }
>>>> balloon click width = 450
>>>> balloon click = <table>
>>>>       <tr><th rowspan="5" align=\"left\"><br>
>>>>       This protein brought to you by <a
>>>> href=\"http://www.expasy.ch\">EXPASY</a>.</th>
>>>>          <th bgcolor=\"cyan\">Gene </th>
>>>>       </tr>
>>>>       <tr align='left'><th><a
>>>> href=\"/cgi-bin/gbrowse_details/motif?name=\">See gene
>>>> details</a></th></tr>
>>>>      <tr align='left'><th><a
>>>> href=\"http://en.wikipedia.org/wiki/Special:Search?search=\">Ask
>>>> Wikipedia about </a></th></tr>
>>>>       <tr align='left'><th><a
>>>> href=\"http://www.google.com/search?q=\">Ask Google about
>>>> </a></th></tr>
>>>>       </table>
>>>>
>>>> key           = pattern
>>>>
>>>>
>>>>
>>>> [profile]
>>>> feature      = profile
>>>> glyph        = so_transcript
>>>> bgcolor      = yellow
>>>> forwardcolor = yellow
>>>> reversecolor = turquoise
>>>> height       = 6
>>>> description  = 0
>>>> balloon hover width = 350
>>>> balloon hover = sub { my  = shift; return join ' ',->notes }
>>>> balloon click width = 450
>>>> balloon click = <table>
>>>>       <tr><th rowspan="5" align=\"left\"><br>
>>>>       This protein brought to you by <a
>>>> href=\"http://www.expasy.ch\">EXPASY</a>.</th>
>>>>           <th bgcolor=\"cyan\">Gene </th>
>>>>      </tr>
>>>>       <tr align='left'><th><a
>>>> href=\"http://en.wikipedia.org/wiki/Special:Search?search=/\">Ask
>>>> Wikipedia about </a></th></tr>
>>>>      <tr align='left'><th><a
>>>> href=\"http://www.google.com/search?q=\">Ask Google about
>>>> </a></th></tr>
>>>>      </table>
>>>> key          = profile";
>>>> fwrite($ourFileHandle, $p);
>>>>
>>>> $url="http://localhost/cgi-bin/gb2/gbrowse/".10190714;
>>>> echo "<br><iframe src =".$url." width="1000" height="700" >
>>>> </iframe>";}
>>>> ?>
>>>>
>>>>
>>>>
>>>> but when I point my browser to
>>>> http://localhost/cgi-bin/gb2/gbrowse/10190714
>>>>
>>>> I get the attached snapshot
>>>>
>>>> On Wed, Sep 24, 2014 at 9:05 AM, umay kulsum <[hidden email]>
>>>> wrote:
>>>> > Hi
>>>> >
>>>> > The error log shows:
>>>> > [cgi:error] [pid 17807] [client 127.0.0.1:34119] AH01215: STACK:
>>>> > /usr/lib/cgi-bin/gb2/gbrowse:55
>>>> >
>>>> > yes I added the entry to /etc/gbrowse/GBrowse.conf
>>>> >
>>>> > On Tue, Sep 23, 2014 at 6:52 PM, Scott Cain <[hidden email]> wrote:
>>>> >> Hi Umay,
>>>> >>
>>>> >> I'm glad you've gotten it working.
>>>> >>
>>>> >> What you're describing with asking for one configuration and getting
>>>> >> another
>>>> >> is what happens when there is a problem with the configuration that you
>>>> >> want.  I don't see anything obvious with the configuration you pasted
>>>> >> into
>>>> >> the email, but my eyes aren't as good a configuration parser as
>>>> >> GBrowse.  A
>>>> >> few questions:
>>>> >>
>>>> >> Do you see anything in the apache error log that indicates that there
>>>> >> is a
>>>> >> problem?
>>>> >>
>>>> >> Did you add an entry for the new configuration file to
>>>> >> /etc/gbrowse/GBrowse.conf?
>>>> >>
>>>> >> Scott
>>>> >>
>>>> >>
>>>> >> On Mon, Sep 22, 2014 at 11:35 PM, umay kulsum <[hidden email]>
>>>> >> wrote:
>>>> >>>
>>>> >>> Hi
>>>> >>>
>>>> >>> Thank you scott....got GBrowse installed with git clone...
>>>> >>> example database of yeast is also working properly...
>>>> >>>
>>>> >>> but now I have created my own conf file as 114635370.conf in
>>>> >>> etc/gbrowse2/gbrowse.conf folder but when I run
>>>> >>> http://localhost/cgi-bin/gb2/gbrowse/114635370 it gives the result of
>>>> >>> yeast but not my own file
>>>> >>> why is it so and what can I do for that??
>>>> >>>
>>>> >>>
>>>> >>> my conf file is as follows:
>>>> >>>
>>>> >>> [GENERAL]
>>>> >>> description   = motifs of 114635370protein
>>>> >>> db_adaptor    = Bio::DB::SeqFeature::Store
>>>> >>> db_args       = -adaptor memory
>>>> >>>                -dir
>>>> >>> '/var/www/html/gbrowse2/databases/1/1/4/114635370/'
>>>> >>>
>>>> >>>
>>>> >>> plugins = BatchDumper FastaDumper
>>>> >>> gbrowse root = gbrowse
>>>> >>> stylesheet   = gbrowse.css
>>>> >>> buttons      = images/buttons
>>>> >>> js           = js
>>>> >>> tmpimages    = tmp
>>>> >>> region segment = 500
>>>> >>> initial landmark = 114635370
>>>> >>> balloon tips    = 1
>>>> >>> drag and drop = 1
>>>> >>> cache time    = 1
>>>> >>> link          = AUTO
>>>> >>> image widths  = 450 640 800 1024
>>>> >>> hilite fill    = beige
>>>> >>> hilite outline = red
>>>> >>> default width = 800
>>>> >>> default features = 114635370
>>>> >>> max segment     = 500
>>>> >>> default segment = 50
>>>> >>> zoom levels    = 50 100 200 1000 2000 5000 10000 20000 40000 100000
>>>> >>> 200000 500000 1000000
>>>> >>> show sources   = 1
>>>> >>> overview bgcolor = lightgrey
>>>> >>> detailed bgcolor = lightgoldenrodyellow
>>>> >>> key bgcolor      = beige
>>>> >>> examples = 114635370
>>>> >>> automatic classes = 114635370
>>>> >>>
>>>> >>>
>>>> >>> [protein]
>>>> >>> feature      = protein
>>>> >>> glyph        = so_transcript
>>>> >>> bgcolor      = yellow
>>>> >>> forwardcolor = yellow
>>>> >>> reversecolor = turquoise
>>>> >>> height       = 6
>>>> >>> description  = 1
>>>> >>> balloon hover width = 350
>>>> >>> balloon hover = sub { my  = shift; return join ' ',->notes }
>>>> >>> balloon click width = 450
>>>> >>> balloon click = <table>
>>>> >>>      <tr><th rowspan="5" align="left"><br>
>>>> >>>      This protein brought to you by <a
>>>> >>> href="http://www.expasy.ch">EXPASY</a>.</th>
>>>> >>>          <th bgcolor="cyan">Gene </th>
>>>> >>>      </tr>
>>>> >>>       <tr align='left'><th><a
>>>> >>> href="/cgi-bin/gbrowse_details/motif?name=">See protein
>>>> >>> details</a></th></tr>
>>>> >>>      <tr align='left'><th><a
>>>> >>> href="http://www.ncbi.nlm.nih.gov/protein/114635370">Go to
>>>> >>> NCBI</a></th></tr>
>>>> >>>       </table>
>>>> >>>
>>>> >>> key          = protein
>>>> >>> [pattern]
>>>> >>> feature      = pattern
>>>> >>> glyph        = so_transcript
>>>> >>> bgcolor      = yellow
>>>> >>> forwardcolor = yellow
>>>> >>> reversecolor = turquoise
>>>> >>> height       = 6
>>>> >>> description  = 1
>>>> >>> balloon hover width = 350
>>>> >>> balloon hover = sub { my  = shift; return join ' ',->notes }
>>>> >>> balloon click width = 450
>>>> >>> balloon click = <table>
>>>> >>>       <tr><th rowspan="5" align="left"><br>
>>>> >>>       This protein brought to you by <a
>>>> >>> href="http://www.expasy.ch">EXPASY</a>.</th>
>>>> >>>          <th bgcolor="cyan">Gene </th>
>>>> >>>       </tr>
>>>> >>>       <tr align='left'><th><a
>>>> >>> href="/cgi-bin/gbrowse_details/motif?name=">See gene
>>>> >>> details</a></th></tr>
>>>> >>>      <tr align='left'><th><a
>>>> >>> href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
>>>> >>> Wikipedia about </a></th></tr>
>>>> >>>       <tr align='left'><th><a
>>>> >>> href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
>>>> >>>       </table>
>>>> >>>
>>>> >>> key           = pattern
>>>> >>>
>>>> >>>
>>>> >>>
>>>> >>> [profile]
>>>> >>> feature      = profile
>>>> >>> glyph        = so_transcript
>>>> >>> bgcolor      = yellow
>>>> >>> forwardcolor = yellow
>>>> >>> reversecolor = turquoise
>>>> >>> height       = 6
>>>> >>> description  = 0
>>>> >>> balloon hover width = 350
>>>> >>> balloon hover = sub { my  = shift; return join ' ',->notes }
>>>> >>> balloon click width = 450
>>>> >>> balloon click = <table>
>>>> >>>       <tr><th rowspan="5" align="left"><br>
>>>> >>>       This protein brought to you by <a
>>>> >>> href="http://www.expasy.ch">EXPASY</a>.</th>
>>>> >>>           <th bgcolor="cyan">Gene </th>
>>>> >>>      </tr>
>>>> >>>       <tr align='left'><th><a
>>>> >>> href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
>>>> >>> Wikipedia about </a></th></tr>
>>>> >>>      <tr align='left'><th><a
>>>> >>> href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
>>>> >>>      </table>
>>>> >>> key          = profile
>>>> >>>
>>>> >>> On Mon, Sep 22, 2014 at 5:36 PM, Scott Cain <[hidden email]>
>>>> >>> wrote:
>>>> >>> > Hi Umay,
>>>> >>> >
>>>> >>> > I don't really know what the problem is--my guess is that there is a
>>>> >>> > network
>>>> >>> > problem.  Can you try from a different network?  Can you clone other
>>>> >>> > things
>>>> >>> > from git but just not GBrowse (I would find that pretty strange if
>>>> >>> > it
>>>> >>> > were
>>>> >>> > the case)?  Also, in case there is a problem with any of the
>>>> >>> > software
>>>> >>> > packages you are using, you should probably run
>>>> >>> >
>>>> >>> >   sudo apt-get update
>>>> >>> >   sudo apt-get upgrade
>>>> >>> >
>>>> >>> > to make sure your system is up to date.
>>>> >>> >
>>>> >>> > Scott
>>>> >>> >
>>>> >>> >
>>>> >>> > On Mon, Sep 22, 2014 at 4:17 AM, umay kulsum <[hidden email]>
>>>> >>> > wrote:
>>>> >>> >>
>>>> >>> >> Hi
>>>> >>> >>
>>>> >>> >> when I do
>>>> >>> >> git clone https://github.com/GMOD/GBrowse.git
>>>> >>> >>
>>>> >>> >> I get the following error:
>>>> >>> >>
>>>> >>> >> Cloning into 'GBrowse'...
>>>> >>> >> fatal: unable to access 'https://github.com/GMOD/GBrowse.git/':
>>>> >>> >> gnutls_handshake() failed: A TLS packet with unexpected length was
>>>> >>> >> received.
>>>> >>> >>
>>>> >>> >> On Thu, Sep 18, 2014 at 7:37 PM, Scott Cain <[hidden email]>
>>>> >>> >> wrote:
>>>> >>> >> > Hi Umay,
>>>> >>> >> >
>>>> >>> >> > I suspect you are using Ubuntu 14.04 (you may have already told
>>>> >>> >> > me
>>>> >>> >> > that--I
>>>> >>> >> > don't remember).  While working recently on some minor bug fixes
>>>> >>> >> > for
>>>> >>> >> > GBrowse, we discovered that when Ubuntu 14.04 was released, they
>>>> >>> >> > dramatically rearranged the file structure for system files,
>>>> >>> >> > which
>>>> >>> >> > broke
>>>> >>> >> > the
>>>> >>> >> > GBrowse installer.  The easiest way to install GBrowse correctly
>>>> >>> >> > at
>>>> >>> >> > the
>>>> >>> >> > moment is to get a GitHub checkout of the current source and
>>>> >>> >> > install
>>>> >>> >> > that
>>>> >>> >> > way.  It's fairly straight forward; this is what you do:
>>>> >>> >> >
>>>> >>> >> > git clone https://github.com/GMOD/GBrowse.git
>>>> >>> >> > cd GBrowse
>>>> >>> >> > perl Build.PL  #accepting the defaults should be fine
>>>> >>> >> > ./Build
>>>> >>> >> > ./Build test
>>>> >>> >> > sudo ./Build install
>>>> >>> >> >
>>>> >>> >> > After doing that you should be able to go to
>>>> >>> >> > http://localhost/gbrowse2
>>>> >>> >> > though the links for sample data sets are written assuming you
>>>> >>> >> > have
>>>> >>> >> > fastcgi
>>>> >>> >> > installed (which is a good idea to use, because it makes things
>>>> >>> >> > faster),
>>>> >>> >> > but
>>>> >>> >> > if you don't have fastcgi, you should still be able to go to
>>>> >>> >> > http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample
>>>> >>> >> > dataset.
>>>> >>> >> > If
>>>> >>> >> > that
>>>> >>> >> > works, you should be able to proceed with the tutorial as well.
>>>> >>> >> >
>>>> >>> >> > On Thu, Sep 18, 2014 at 2:15 AM, umay kulsum
>>>> >>> >> > <[hidden email]>
>>>> >>> >> > wrote:
>>>> >>> >> >>
>>>> >>> >> >> whenever we write localhost it looks for files in /var/www/html
>>>> >>> >> >> so I think its looking for /cgi-bin/gb2/gbrowse/yeast in
>>>> >>> >> >> /var/www
>>>> >>> >> >>
>>>> >>> >> >> On Thu, Sep 18, 2014 at 11:25 AM, umay kulsum
>>>> >>> >> >> <[hidden email]>
>>>> >>> >> >> wrote:
>>>> >>> >> >> > The apache error log shows :
>>>> >>> >> >> >
>>>> >>> >> >> > [Thu Sep 18 09:03:14.584273 2014] [core:notice] [pid 10766]
>>>> >>> >> >> > AH00094:
>>>> >>> >> >> > Command line: '/usr/sbin/apache2'
>>>> >>> >> >> >
>>>> >>> >> >> >
>>>> >>> >> >> > This is the last comment in /var/log/apache2/error.log......
>>>> >>> >> >> > it
>>>> >>> >> >> > shows
>>>> >>> >> >> > nothing regarding the files not found
>>>> >>> >> >> >
>>>> >>> >> >> >
>>>> >>> >> >> > In the access.log file the last comment is :
>>>> >>> >> >> >
>>>> >>> >> >> >
>>>> >>> >> >> > 127.0.0.1 - - [18/Sep/2014:11:13:58 +0530] "GET
>>>> >>> >> >> > /cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513 "-" "Mozilla/5.0
>>>> >>> >> >> > (X11;
>>>> >>> >> >> > Ubuntu; Linux x86_64; rv:28.0) Gecko/20100101 Firefox/28.0"
>>>> >>> >> >> >
>>>> >>> >> >> > On Thu, Sep 18, 2014 at 10:34 AM, Scott Cain
>>>> >>> >> >> > <[hidden email]>
>>>> >>> >> >> > wrote:
>>>> >>> >> >> >> Hi Umay,
>>>> >>> >> >> >>
>>>> >>> >> >> >> What does it say in the apache error log?  If you're getting
>>>> >>> >> >> >> a
>>>> >>> >> >> >> message
>>>> >>> >> >> >> about a file not being found, it will record where it was
>>>> >>> >> >> >> looking
>>>> >>> >> >> >> for the
>>>> >>> >> >> >> file. The error log is in /var/log/apache2. The most recent
>>>> >>> >> >> >> message
>>>> >>> >> >> >> is at
>>>> >>> >> >> >> the end of the file.
>>>> >>> >> >> >>
>>>> >>> >> >> >> Scott
>>>> >>> >> >> >>
>>>> >>> >> >> >>
>>>> >>> >> >> >> Sent from my iPhone
>>>> >>> >> >> >>
>>>> >>> >> >> >>> On Sep 17, 2014, at 11:03 PM, umay kulsum
>>>> >>> >> >> >>> <[hidden email]>
>>>> >>> >> >> >>> wrote:
>>>> >>> >> >> >>>
>>>> >>> >> >> >>> hi
>>>> >>> >> >> >>> I have tried http://localhost/cgi-bin/gb2/gbrowse/yeast also
>>>> >>> >> >> >>> but
>>>> >>> >> >> >>> again
>>>> >>> >> >> >>> its the same the requested url is not found on the server...
>>>> >>> >> >> >>> what should I do??
>>>> >>> >> >> >>> where am I going wrong??
>>>> >>> >> >> >>> can you please tell me how can I start from scratch that is
>>>> >>> >> >> >>> uninstall
>>>> >>> >> >> >>> and then reinstall....
>>>> >>> >> >> >>>
>>>> >>> >> >> >>>> On Wed, Sep 17, 2014 at 7:47 PM, Scott Cain
>>>> >>> >> >> >>>> <[hidden email]>
>>>> >>> >> >> >>>> wrote:
>>>> >>> >> >> >>>> Umay,
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>> Please "reply-all" so that your replies stay on the GBrowse
>>>> >>> >> >> >>>> mailing
>>>> >>> >> >> >>>> list.
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>> A few things:
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>> The url you are using is not correct; it should be
>>>> >>> >> >> >>>> http://localhost/cgi-bin/gb2/gbrowse/yeast.  This is linked
>>>> >>> >> >> >>>> to
>>>> >>> >> >> >>>> from
>>>> >>> >> >> >>>> http://localhost/gbrowse2/
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>> I don't know why you have two yeast_chr1+2 directories, but
>>>> >>> >> >> >>>> only
>>>> >>> >> >> >>>> one
>>>> >>> >> >> >>>> of them
>>>> >>> >> >> >>>> will work.  The typical configuration would be for the one
>>>> >>> >> >> >>>> in
>>>> >>> >> >> >>>> /var/lib/gbrowse2/databases to work.
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>> The cgi-bin directory is not in the /var/www directory when
>>>> >>> >> >> >>>> apache
>>>> >>> >> >> >>>> is
>>>> >>> >> >> >>>> typically configured for ubuntu; it's in /usr/lib/cgi-bin,
>>>> >>> >> >> >>>> as
>>>> >>> >> >> >>>> it
>>>> >>> >> >> >>>> is
>>>> >>> >> >> >>>> in your
>>>> >>> >> >> >>>> case.
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>> Scott
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>>> On Wed, Sep 17, 2014 at 4:15 AM, umay kulsum
>>>> >>> >> >> >>>>> <[hidden email]>
>>>> >>> >> >> >>>>> wrote:
>>>> >>> >> >> >>>>>
>>>> >>> >> >> >>>>> I have installed GBrowse using the command in ubuntu 14.04
>>>> >>> >> >> >>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>>>> >>> >> >> >>>>>
>>>> >>> >> >> >>>>> I have the following files:
>>>> >>> >> >> >>>>> etc/gbrowse2/GBrowse.conf
>>>> >>> >> >> >>>>> var/www/gbrowse2/databases where I have the yeast_chr1+2
>>>> >>> >> >> >>>>> folder
>>>> >>> >> >> >>>>> with
>>>> >>> >> >> >>>>> my own data files
>>>> >>> >> >> >>>>> usr/lib/cgi-bin/gb2
>>>> >>> >> >> >>>>> var/lib/gbrowse2/databases/yeast_chr1+2 with other files
>>>> >>> >> >> >>>>>
>>>> >>> >> >> >>>>> but still the url http://localhost/cgi-bin/gbrowse2/yeast
>>>> >>> >> >> >>>>> shows
>>>> >>> >> >> >>>>> the
>>>> >>> >> >> >>>>> following url was not found on the server
>>>> >>> >> >> >>>>>
>>>> >>> >> >> >>>>> where is the cgi-bin mentioned in the url located when it
>>>> >>> >> >> >>>>> is
>>>> >>> >> >> >>>>> not
>>>> >>> >> >> >>>>> in
>>>> >>> >> >> >>>>> /var/www/
>>>> >>> >> >> >>>>>
>>>> >>> >> >> >>>>> On Wed, Sep 17, 2014 at 8:54 AM, umay kulsum
>>>> >>> >> >> >>>>> <[hidden email]>
>>>> >>> >> >> >>>>> wrote:
>>>> >>> >> >> >>>>>> Hi
>>>> >>> >> >> >>>>>> I have installed GBrowse using the command in ubuntu
>>>> >>> >> >> >>>>>> 14.04
>>>> >>> >> >> >>>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>>>> >>> >> >> >>>>>> but when I point my browser to
>>>> >>> >> >> >>>>>> http://localhost/cgi-bin/gbrowse2/yeast, it shows the
>>>> >>> >> >> >>>>>> following
>>>> >>> >> >> >>>>>> url
>>>> >>> >> >> >>>>>> is
>>>> >>> >> >> >>>>>> not found on this server..
>>>> >>> >> >> >>>>>> where is the cgi-bin mentioned in the url located when it
>>>> >>> >> >> >>>>>> is
>>>> >>> >> >> >>>>>> not
>>>> >>> >> >> >>>>>> in
>>>> >>> >> >> >>>>>> /var/www/
>>>> >>> >> >> >>>>>>
>>>> >>> >> >> >>>>>>> On Tue, Sep 16, 2014 at 2:28 AM, Scott Cain
>>>> >>> >> >> >>>>>>> <[hidden email]>
>>>> >>> >> >> >>>>>>> wrote:
>>>> >>> >> >> >>>>>>> Hi Umay,
>>>> >>> >> >> >>>>>>>
>>>> >>> >> >> >>>>>>> Can you please tell us what you done and where you think
>>>> >>> >> >> >>>>>>> the
>>>> >>> >> >> >>>>>>> process
>>>> >>> >> >> >>>>>>> has failed?  For instance, what do you see when you go
>>>> >>> >> >> >>>>>>> to
>>>> >>> >> >> >>>>>>> the
>>>> >>> >> >> >>>>>>> built in
>>>> >>> >> >> >>>>>>> sample yeast data set?
>>>> >>> >> >> >>>>>>>
>>>> >>> >> >> >>>>>>> Scott
>>>> >>> >> >> >>>>>>>
>>>> >>> >> >> >>>>>>> Sent from my iPhone
>>>> >>> >> >> >>>>>>>
>>>> >>> >> >> >>>>>>>> On Sep 11, 2014, at 11:41 PM, umay kulsum
>>>> >>> >> >> >>>>>>>> <[hidden email]>
>>>> >>> >> >> >>>>>>>> wrote:
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>> I have been trying to install and invoke GBrowse since
>>>> >>> >> >> >>>>>>>> a
>>>> >>> >> >> >>>>>>>> month
>>>> >>> >> >> >>>>>>>> but to
>>>> >>> >> >> >>>>>>>> no result....
>>>> >>> >> >> >>>>>>>> can someone help me regarding the installation process.
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>> ------------------------------------------------------------------------------
>>>> >>> >> >> >>>>>>>> Want excitement?
>>>> >>> >> >> >>>>>>>> Manually upgrade your production database.
>>>> >>> >> >> >>>>>>>> When you want reliability, choose Perforce
>>>> >>> >> >> >>>>>>>> Perforce version control. Predictably reliable.
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
>>>> >>> >> >> >>>>>>>> _______________________________________________
>>>> >>> >> >> >>>>>>>> Gmod-gbrowse mailing list
>>>> >>> >> >> >>>>>>>> [hidden email]
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>> --
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>> ------------------------------------------------------------------------
>>>> >>> >> >> >>>> Scott Cain, Ph. D.                                   scott
>>>> >>> >> >> >>>> at
>>>> >>> >> >> >>>> scottcain dot
>>>> >>> >> >> >>>> net
>>>> >>> >> >> >>>> GMOD Coordinator (http://gmod.org/)
>>>> >>> >> >> >>>> 216-392-3087
>>>> >>> >> >> >>>> Ontario Institute for Cancer Research
>>>> >>> >> >
>>>> >>> >> >
>>>> >>> >> >
>>>> >>> >> >
>>>> >>> >> > --
>>>> >>> >> >
>>>> >>> >> >
>>>> >>> >> > ------------------------------------------------------------------------
>>>> >>> >> > Scott Cain, Ph. D.                                   scott at
>>>> >>> >> > scottcain
>>>> >>> >> > dot
>>>> >>> >> > net
>>>> >>> >> > GMOD Coordinator (http://gmod.org/)
>>>> >>> >> > 216-392-3087
>>>> >>> >> > Ontario Institute for Cancer Research
>>>> >>> >
>>>> >>> >
>>>> >>> >
>>>> >>> >
>>>> >>> > --
>>>> >>> >
>>>> >>> > ------------------------------------------------------------------------
>>>> >>> > Scott Cain, Ph. D.                                   scott at
>>>> >>> > scottcain
>>>> >>> > dot
>>>> >>> > net
>>>> >>> > GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> >>> > Ontario Institute for Cancer Research
>>>> >>
>>>> >>
>>>> >>
>>>> >>
>>>> >> --
>>>> >>
>>>> >> ------------------------------------------------------------------------
>>>> >> Scott Cain, Ph. D.                                   scott at scottcain
>>>> >> dot
>>>> >> net
>>>> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> >> Ontario Institute for Cancer Research
>>>
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot
>>> net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research

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Re: help regarding gbrowse

Scott Cain
Hi Umay,

The chown command changed the GFF file from text to binary? It's not often I say things are impossible, but that's pretty close.  How do you know it changed it to binary?  Are you sure it's binary now?

As for the screenshot you included, it shows that there are still problems with your configuration: I suspect that gbrowse still can't find various files it needs to work correctly, like css and javascript files.  Please look at your apache access log for 404 errors to see where it is looking for files and try to figure out why it's looking in the wrong place.

Scott


On Fri, Sep 26, 2014 at 12:22 AM, umay kulsum <[hidden email]> wrote:
Hi Scott

I have done as you directed. The error message is no more there but
not getting the tracks.
screenshot is attached.
and the gff3 file is not being displayed when I open
/var/lib/gbrowse2/databases.
the gff3 file is also attached.

The command chown -R www-data:www-data changes the gff3 file from
plain text to binary
The original gff3 is also attached

On Fri, Sep 26, 2014 at 9:17 AM, umay kulsum <[hidden email]> wrote:
> Hi Scott
>
> I have done as you directed. The error message is no more there but
> not getting the tracks.
> screenshot is attached.
> and the gff3 file is not being displayed when I open
> /var/lib/gbrowse2/databases.
> the gff3 file is also attached.
>
> On Fri, Sep 26, 2014 at 8:35 AM, umay kulsum <[hidden email]> wrote:
>> Hi Scott,
>>
>> I have done as you directed. The error message is no more there but
>> not getting the tracks.
>> screenshot is attached.
>>
>>
>>
>> On Wed, Sep 24, 2014 at 8:33 PM, Scott Cain <[hidden email]> wrote:
>>> Hi Umay,
>>>
>>> That message at the top of the screenshot you sent is the full error
>>> message.  The first line of it has the source of the problem.  It can't open
>>> the file at /var/lib/gbrowse2/databases/1......  Does that directory exist
>>> and does the webserver have permission to open it?  Probably the best thing
>>> to do is to change ownership of that directory to the user that runs the
>>> webserver:
>>>
>>>   sudo chown -R www-data:www-data /var/lib/gbrowse2/databases/*
>>>
>>> If you're making frequent edits in the databases directories (like when
>>> you're doing the tutorial), you can just make the directory you're working
>>> on world writeable, so that the webserver and you can both write files in
>>> the directory without sudo.  Of course, this is considerably less secure:
>>>
>>>   sudo chmod -R a+w /var/lib/gbrowse2/databases/nameofdatabase
>>>
>>> Scott
>>>
>>>
>>> On Tue, Sep 23, 2014 at 11:52 PM, umay kulsum <[hidden email]> wrote:
>>>>
>>>> hi Scott
>>>>
>>>> I have created a script gbtry.php which is as follows:
>>>>
>>>> <?php
>>>> $ourFileName = "/etc/gbrowse2/gbrowse.conf/".10190714.".conf";
>>>> $ourFileHandle = fopen($ourFileName, 'w') or die("can't open file");
>>>> $p="[GENERAL]
>>>> description   = motifs of ".21105857."protein
>>>> db_adaptor    = Bio::DB::SeqFeature::Store
>>>> db_args       = -adaptor memory
>>>>                -dir    '/var/www/html/gbrowse2/databases/10190714'
>>>>
>>>>
>>>> plugins = BatchDumper FastaDumper
>>>> gbrowse root = gbrowse
>>>> stylesheet   = gbrowse.css
>>>> buttons      = images/buttons
>>>> js           = js
>>>> tmpimages    = tmp
>>>> region segment = 500
>>>> initial landmark = \".21105857.\"
>>>> balloon tips    = 1
>>>> drag and drop = 1
>>>> cache time    = 1
>>>> link          = AUTO
>>>> image widths  = 450 640 800 1024
>>>> hilite fill    = beige
>>>> hilite outline = red
>>>> default width = 800
>>>> default features = \".21105857.\"
>>>> max segment     = 500
>>>> default segment = 50
>>>> zoom levels    = 50 100 200 1000 2000 5000 10000 20000 40000 100000
>>>> 200000 500000 1000000
>>>> show sources   = 1
>>>> overview bgcolor = lightgrey
>>>> detailed bgcolor = lightgoldenrodyellow
>>>> key bgcolor      = beige
>>>> examples =\".21105857.\"
>>>> automatic classes = \".21105857.\"
>>>>
>>>>
>>>> [protein]
>>>> feature      = protein
>>>> glyph        = so_transcript
>>>> bgcolor      = yellow
>>>> forwardcolor = yellow
>>>> reversecolor = turquoise
>>>> height       = 6
>>>> description  = 1
>>>> balloon hover width = 350
>>>> balloon hover = sub { my  = shift; return join ' ',->notes }
>>>> balloon click width = 450
>>>> balloon click = <table>
>>>>      <tr><th rowspan="5" align=\"left\"><br>
>>>>      This protein brought to you by <a
>>>> href=\"http://www.expasy.ch\">EXPASY</a>.</th>
>>>>          <th bgcolor=\"cyan\">Gene </th>
>>>>      </tr>
>>>>       <tr align='left'><th><a
>>>> href=\"/cgi-bin/gbrowse_details/motif?name=\">See protein
>>>> details</a></th></tr>
>>>>      <tr align='left'><th><a
>>>> href=\"<a href="http://www.ncbi.nlm.nih.gov/protein/\" target="_blank">http://www.ncbi.nlm.nih.gov/protein/\".21105857."">Go to
>>>> NCBI</a></th></tr>
>>>>       </table>
>>>>
>>>> key          = protein
>>>> [pattern]
>>>> feature      = pattern
>>>> glyph        = so_transcript
>>>> bgcolor      = yellow
>>>> forwardcolor = yellow
>>>> reversecolor = turquoise
>>>> height       = 6
>>>> description  = 1
>>>> balloon hover width = 350
>>>> balloon hover = sub { my  = shift; return join ' ',->notes }
>>>> balloon click width = 450
>>>> balloon click = <table>
>>>>       <tr><th rowspan="5" align=\"left\"><br>
>>>>       This protein brought to you by <a
>>>> href=\"http://www.expasy.ch\">EXPASY</a>.</th>
>>>>          <th bgcolor=\"cyan\">Gene </th>
>>>>       </tr>
>>>>       <tr align='left'><th><a
>>>> href=\"/cgi-bin/gbrowse_details/motif?name=\">See gene
>>>> details</a></th></tr>
>>>>      <tr align='left'><th><a
>>>> href=\"<a href="http://en.wikipedia.org/wiki/Special:Search?search=\" target="_blank">http://en.wikipedia.org/wiki/Special:Search?search=\">Ask
>>>> Wikipedia about </a></th></tr>
>>>>       <tr align='left'><th><a
>>>> href=\"<a href="http://www.google.com/search?q=\" target="_blank">http://www.google.com/search?q=\">Ask Google about
>>>> </a></th></tr>
>>>>       </table>
>>>>
>>>> key           = pattern
>>>>
>>>>
>>>>
>>>> [profile]
>>>> feature      = profile
>>>> glyph        = so_transcript
>>>> bgcolor      = yellow
>>>> forwardcolor = yellow
>>>> reversecolor = turquoise
>>>> height       = 6
>>>> description  = 0
>>>> balloon hover width = 350
>>>> balloon hover = sub { my  = shift; return join ' ',->notes }
>>>> balloon click width = 450
>>>> balloon click = <table>
>>>>       <tr><th rowspan="5" align=\"left\"><br>
>>>>       This protein brought to you by <a
>>>> href=\"http://www.expasy.ch\">EXPASY</a>.</th>
>>>>           <th bgcolor=\"cyan\">Gene </th>
>>>>      </tr>
>>>>       <tr align='left'><th><a
>>>> href=\"<a href="http://en.wikipedia.org/wiki/Special:Search?search=/\" target="_blank">http://en.wikipedia.org/wiki/Special:Search?search=/\">Ask
>>>> Wikipedia about </a></th></tr>
>>>>      <tr align='left'><th><a
>>>> href=\"<a href="http://www.google.com/search?q=\" target="_blank">http://www.google.com/search?q=\">Ask Google about
>>>> </a></th></tr>
>>>>      </table>
>>>> key          = profile";
>>>> fwrite($ourFileHandle, $p);
>>>>
>>>> $url="http://localhost/cgi-bin/gb2/gbrowse/".10190714;
>>>> echo "<br><iframe src =".$url." width="1000" height="700" >
>>>> </iframe>";}
>>>> ?>
>>>>
>>>>
>>>>
>>>> but when I point my browser to
>>>> http://localhost/cgi-bin/gb2/gbrowse/10190714
>>>>
>>>> I get the attached snapshot
>>>>
>>>> On Wed, Sep 24, 2014 at 9:05 AM, umay kulsum <[hidden email]>
>>>> wrote:
>>>> > Hi
>>>> >
>>>> > The error log shows:
>>>> > [cgi:error] [pid 17807] [client 127.0.0.1:34119] AH01215: STACK:
>>>> > /usr/lib/cgi-bin/gb2/gbrowse:55
>>>> >
>>>> > yes I added the entry to /etc/gbrowse/GBrowse.conf
>>>> >
>>>> > On Tue, Sep 23, 2014 at 6:52 PM, Scott Cain <[hidden email]> wrote:
>>>> >> Hi Umay,
>>>> >>
>>>> >> I'm glad you've gotten it working.
>>>> >>
>>>> >> What you're describing with asking for one configuration and getting
>>>> >> another
>>>> >> is what happens when there is a problem with the configuration that you
>>>> >> want.  I don't see anything obvious with the configuration you pasted
>>>> >> into
>>>> >> the email, but my eyes aren't as good a configuration parser as
>>>> >> GBrowse.  A
>>>> >> few questions:
>>>> >>
>>>> >> Do you see anything in the apache error log that indicates that there
>>>> >> is a
>>>> >> problem?
>>>> >>
>>>> >> Did you add an entry for the new configuration file to
>>>> >> /etc/gbrowse/GBrowse.conf?
>>>> >>
>>>> >> Scott
>>>> >>
>>>> >>
>>>> >> On Mon, Sep 22, 2014 at 11:35 PM, umay kulsum <[hidden email]>
>>>> >> wrote:
>>>> >>>
>>>> >>> Hi
>>>> >>>
>>>> >>> Thank you scott....got GBrowse installed with git clone...
>>>> >>> example database of yeast is also working properly...
>>>> >>>
>>>> >>> but now I have created my own conf file as 114635370.conf in
>>>> >>> etc/gbrowse2/gbrowse.conf folder but when I run
>>>> >>> http://localhost/cgi-bin/gb2/gbrowse/114635370 it gives the result of
>>>> >>> yeast but not my own file
>>>> >>> why is it so and what can I do for that??
>>>> >>>
>>>> >>>
>>>> >>> my conf file is as follows:
>>>> >>>
>>>> >>> [GENERAL]
>>>> >>> description   = motifs of 114635370protein
>>>> >>> db_adaptor    = Bio::DB::SeqFeature::Store
>>>> >>> db_args       = -adaptor memory
>>>> >>>                -dir
>>>> >>> '/var/www/html/gbrowse2/databases/1/1/4/114635370/'
>>>> >>>
>>>> >>>
>>>> >>> plugins = BatchDumper FastaDumper
>>>> >>> gbrowse root = gbrowse
>>>> >>> stylesheet   = gbrowse.css
>>>> >>> buttons      = images/buttons
>>>> >>> js           = js
>>>> >>> tmpimages    = tmp
>>>> >>> region segment = 500
>>>> >>> initial landmark = 114635370
>>>> >>> balloon tips    = 1
>>>> >>> drag and drop = 1
>>>> >>> cache time    = 1
>>>> >>> link          = AUTO
>>>> >>> image widths  = 450 640 800 1024
>>>> >>> hilite fill    = beige
>>>> >>> hilite outline = red
>>>> >>> default width = 800
>>>> >>> default features = 114635370
>>>> >>> max segment     = 500
>>>> >>> default segment = 50
>>>> >>> zoom levels    = 50 100 200 1000 2000 5000 10000 20000 40000 100000
>>>> >>> 200000 500000 1000000
>>>> >>> show sources   = 1
>>>> >>> overview bgcolor = lightgrey
>>>> >>> detailed bgcolor = lightgoldenrodyellow
>>>> >>> key bgcolor      = beige
>>>> >>> examples = 114635370
>>>> >>> automatic classes = 114635370
>>>> >>>
>>>> >>>
>>>> >>> [protein]
>>>> >>> feature      = protein
>>>> >>> glyph        = so_transcript
>>>> >>> bgcolor      = yellow
>>>> >>> forwardcolor = yellow
>>>> >>> reversecolor = turquoise
>>>> >>> height       = 6
>>>> >>> description  = 1
>>>> >>> balloon hover width = 350
>>>> >>> balloon hover = sub { my  = shift; return join ' ',->notes }
>>>> >>> balloon click width = 450
>>>> >>> balloon click = <table>
>>>> >>>      <tr><th rowspan="5" align="left"><br>
>>>> >>>      This protein brought to you by <a
>>>> >>> href="http://www.expasy.ch">EXPASY</a>.</th>
>>>> >>>          <th bgcolor="cyan">Gene </th>
>>>> >>>      </tr>
>>>> >>>       <tr align='left'><th><a
>>>> >>> href="/cgi-bin/gbrowse_details/motif?name=">See protein
>>>> >>> details</a></th></tr>
>>>> >>>      <tr align='left'><th><a
>>>> >>> href="http://www.ncbi.nlm.nih.gov/protein/114635370">Go to
>>>> >>> NCBI</a></th></tr>
>>>> >>>       </table>
>>>> >>>
>>>> >>> key          = protein
>>>> >>> [pattern]
>>>> >>> feature      = pattern
>>>> >>> glyph        = so_transcript
>>>> >>> bgcolor      = yellow
>>>> >>> forwardcolor = yellow
>>>> >>> reversecolor = turquoise
>>>> >>> height       = 6
>>>> >>> description  = 1
>>>> >>> balloon hover width = 350
>>>> >>> balloon hover = sub { my  = shift; return join ' ',->notes }
>>>> >>> balloon click width = 450
>>>> >>> balloon click = <table>
>>>> >>>       <tr><th rowspan="5" align="left"><br>
>>>> >>>       This protein brought to you by <a
>>>> >>> href="http://www.expasy.ch">EXPASY</a>.</th>
>>>> >>>          <th bgcolor="cyan">Gene </th>
>>>> >>>       </tr>
>>>> >>>       <tr align='left'><th><a
>>>> >>> href="/cgi-bin/gbrowse_details/motif?name=">See gene
>>>> >>> details</a></th></tr>
>>>> >>>      <tr align='left'><th><a
>>>> >>> href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
>>>> >>> Wikipedia about </a></th></tr>
>>>> >>>       <tr align='left'><th><a
>>>> >>> href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
>>>> >>>       </table>
>>>> >>>
>>>> >>> key           = pattern
>>>> >>>
>>>> >>>
>>>> >>>
>>>> >>> [profile]
>>>> >>> feature      = profile
>>>> >>> glyph        = so_transcript
>>>> >>> bgcolor      = yellow
>>>> >>> forwardcolor = yellow
>>>> >>> reversecolor = turquoise
>>>> >>> height       = 6
>>>> >>> description  = 0
>>>> >>> balloon hover width = 350
>>>> >>> balloon hover = sub { my  = shift; return join ' ',->notes }
>>>> >>> balloon click width = 450
>>>> >>> balloon click = <table>
>>>> >>>       <tr><th rowspan="5" align="left"><br>
>>>> >>>       This protein brought to you by <a
>>>> >>> href="http://www.expasy.ch">EXPASY</a>.</th>
>>>> >>>           <th bgcolor="cyan">Gene </th>
>>>> >>>      </tr>
>>>> >>>       <tr align='left'><th><a
>>>> >>> href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
>>>> >>> Wikipedia about </a></th></tr>
>>>> >>>      <tr align='left'><th><a
>>>> >>> href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
>>>> >>>      </table>
>>>> >>> key          = profile
>>>> >>>
>>>> >>> On Mon, Sep 22, 2014 at 5:36 PM, Scott Cain <[hidden email]>
>>>> >>> wrote:
>>>> >>> > Hi Umay,
>>>> >>> >
>>>> >>> > I don't really know what the problem is--my guess is that there is a
>>>> >>> > network
>>>> >>> > problem.  Can you try from a different network?  Can you clone other
>>>> >>> > things
>>>> >>> > from git but just not GBrowse (I would find that pretty strange if
>>>> >>> > it
>>>> >>> > were
>>>> >>> > the case)?  Also, in case there is a problem with any of the
>>>> >>> > software
>>>> >>> > packages you are using, you should probably run
>>>> >>> >
>>>> >>> >   sudo apt-get update
>>>> >>> >   sudo apt-get upgrade
>>>> >>> >
>>>> >>> > to make sure your system is up to date.
>>>> >>> >
>>>> >>> > Scott
>>>> >>> >
>>>> >>> >
>>>> >>> > On Mon, Sep 22, 2014 at 4:17 AM, umay kulsum <[hidden email]>
>>>> >>> > wrote:
>>>> >>> >>
>>>> >>> >> Hi
>>>> >>> >>
>>>> >>> >> when I do
>>>> >>> >> git clone https://github.com/GMOD/GBrowse.git
>>>> >>> >>
>>>> >>> >> I get the following error:
>>>> >>> >>
>>>> >>> >> Cloning into 'GBrowse'...
>>>> >>> >> fatal: unable to access 'https://github.com/GMOD/GBrowse.git/':
>>>> >>> >> gnutls_handshake() failed: A TLS packet with unexpected length was
>>>> >>> >> received.
>>>> >>> >>
>>>> >>> >> On Thu, Sep 18, 2014 at 7:37 PM, Scott Cain <[hidden email]>
>>>> >>> >> wrote:
>>>> >>> >> > Hi Umay,
>>>> >>> >> >
>>>> >>> >> > I suspect you are using Ubuntu 14.04 (you may have already told
>>>> >>> >> > me
>>>> >>> >> > that--I
>>>> >>> >> > don't remember).  While working recently on some minor bug fixes
>>>> >>> >> > for
>>>> >>> >> > GBrowse, we discovered that when Ubuntu 14.04 was released, they
>>>> >>> >> > dramatically rearranged the file structure for system files,
>>>> >>> >> > which
>>>> >>> >> > broke
>>>> >>> >> > the
>>>> >>> >> > GBrowse installer.  The easiest way to install GBrowse correctly
>>>> >>> >> > at
>>>> >>> >> > the
>>>> >>> >> > moment is to get a GitHub checkout of the current source and
>>>> >>> >> > install
>>>> >>> >> > that
>>>> >>> >> > way.  It's fairly straight forward; this is what you do:
>>>> >>> >> >
>>>> >>> >> > git clone https://github.com/GMOD/GBrowse.git
>>>> >>> >> > cd GBrowse
>>>> >>> >> > perl Build.PL  #accepting the defaults should be fine
>>>> >>> >> > ./Build
>>>> >>> >> > ./Build test
>>>> >>> >> > sudo ./Build install
>>>> >>> >> >
>>>> >>> >> > After doing that you should be able to go to
>>>> >>> >> > http://localhost/gbrowse2
>>>> >>> >> > though the links for sample data sets are written assuming you
>>>> >>> >> > have
>>>> >>> >> > fastcgi
>>>> >>> >> > installed (which is a good idea to use, because it makes things
>>>> >>> >> > faster),
>>>> >>> >> > but
>>>> >>> >> > if you don't have fastcgi, you should still be able to go to
>>>> >>> >> > http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample
>>>> >>> >> > dataset.
>>>> >>> >> > If
>>>> >>> >> > that
>>>> >>> >> > works, you should be able to proceed with the tutorial as well.
>>>> >>> >> >
>>>> >>> >> > On Thu, Sep 18, 2014 at 2:15 AM, umay kulsum
>>>> >>> >> > <[hidden email]>
>>>> >>> >> > wrote:
>>>> >>> >> >>
>>>> >>> >> >> whenever we write localhost it looks for files in /var/www/html
>>>> >>> >> >> so I think its looking for /cgi-bin/gb2/gbrowse/yeast in
>>>> >>> >> >> /var/www
>>>> >>> >> >>
>>>> >>> >> >> On Thu, Sep 18, 2014 at 11:25 AM, umay kulsum
>>>> >>> >> >> <[hidden email]>
>>>> >>> >> >> wrote:
>>>> >>> >> >> > The apache error log shows :
>>>> >>> >> >> >
>>>> >>> >> >> > [Thu Sep 18 09:03:14.584273 2014] [core:notice] [pid 10766]
>>>> >>> >> >> > AH00094:
>>>> >>> >> >> > Command line: '/usr/sbin/apache2'
>>>> >>> >> >> >
>>>> >>> >> >> >
>>>> >>> >> >> > This is the last comment in /var/log/apache2/error.log......
>>>> >>> >> >> > it
>>>> >>> >> >> > shows
>>>> >>> >> >> > nothing regarding the files not found
>>>> >>> >> >> >
>>>> >>> >> >> >
>>>> >>> >> >> > In the access.log file the last comment is :
>>>> >>> >> >> >
>>>> >>> >> >> >
>>>> >>> >> >> > 127.0.0.1 - - [18/Sep/2014:11:13:58 +0530] "GET
>>>> >>> >> >> > /cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513 "-" "Mozilla/5.0
>>>> >>> >> >> > (X11;
>>>> >>> >> >> > Ubuntu; Linux x86_64; rv:28.0) Gecko/20100101 Firefox/28.0"
>>>> >>> >> >> >
>>>> >>> >> >> > On Thu, Sep 18, 2014 at 10:34 AM, Scott Cain
>>>> >>> >> >> > <[hidden email]>
>>>> >>> >> >> > wrote:
>>>> >>> >> >> >> Hi Umay,
>>>> >>> >> >> >>
>>>> >>> >> >> >> What does it say in the apache error log?  If you're getting
>>>> >>> >> >> >> a
>>>> >>> >> >> >> message
>>>> >>> >> >> >> about a file not being found, it will record where it was
>>>> >>> >> >> >> looking
>>>> >>> >> >> >> for the
>>>> >>> >> >> >> file. The error log is in /var/log/apache2. The most recent
>>>> >>> >> >> >> message
>>>> >>> >> >> >> is at
>>>> >>> >> >> >> the end of the file.
>>>> >>> >> >> >>
>>>> >>> >> >> >> Scott
>>>> >>> >> >> >>
>>>> >>> >> >> >>
>>>> >>> >> >> >> Sent from my iPhone
>>>> >>> >> >> >>
>>>> >>> >> >> >>> On Sep 17, 2014, at 11:03 PM, umay kulsum
>>>> >>> >> >> >>> <[hidden email]>
>>>> >>> >> >> >>> wrote:
>>>> >>> >> >> >>>
>>>> >>> >> >> >>> hi
>>>> >>> >> >> >>> I have tried http://localhost/cgi-bin/gb2/gbrowse/yeast also
>>>> >>> >> >> >>> but
>>>> >>> >> >> >>> again
>>>> >>> >> >> >>> its the same the requested url is not found on the server...
>>>> >>> >> >> >>> what should I do??
>>>> >>> >> >> >>> where am I going wrong??
>>>> >>> >> >> >>> can you please tell me how can I start from scratch that is
>>>> >>> >> >> >>> uninstall
>>>> >>> >> >> >>> and then reinstall....
>>>> >>> >> >> >>>
>>>> >>> >> >> >>>> On Wed, Sep 17, 2014 at 7:47 PM, Scott Cain
>>>> >>> >> >> >>>> <[hidden email]>
>>>> >>> >> >> >>>> wrote:
>>>> >>> >> >> >>>> Umay,
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>> Please "reply-all" so that your replies stay on the GBrowse
>>>> >>> >> >> >>>> mailing
>>>> >>> >> >> >>>> list.
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>> A few things:
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>> The url you are using is not correct; it should be
>>>> >>> >> >> >>>> http://localhost/cgi-bin/gb2/gbrowse/yeast.  This is linked
>>>> >>> >> >> >>>> to
>>>> >>> >> >> >>>> from
>>>> >>> >> >> >>>> http://localhost/gbrowse2/
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>> I don't know why you have two yeast_chr1+2 directories, but
>>>> >>> >> >> >>>> only
>>>> >>> >> >> >>>> one
>>>> >>> >> >> >>>> of them
>>>> >>> >> >> >>>> will work.  The typical configuration would be for the one
>>>> >>> >> >> >>>> in
>>>> >>> >> >> >>>> /var/lib/gbrowse2/databases to work.
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>> The cgi-bin directory is not in the /var/www directory when
>>>> >>> >> >> >>>> apache
>>>> >>> >> >> >>>> is
>>>> >>> >> >> >>>> typically configured for ubuntu; it's in /usr/lib/cgi-bin,
>>>> >>> >> >> >>>> as
>>>> >>> >> >> >>>> it
>>>> >>> >> >> >>>> is
>>>> >>> >> >> >>>> in your
>>>> >>> >> >> >>>> case.
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>> Scott
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>>> On Wed, Sep 17, 2014 at 4:15 AM, umay kulsum
>>>> >>> >> >> >>>>> <[hidden email]>
>>>> >>> >> >> >>>>> wrote:
>>>> >>> >> >> >>>>>
>>>> >>> >> >> >>>>> I have installed GBrowse using the command in ubuntu 14.04
>>>> >>> >> >> >>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>>>> >>> >> >> >>>>>
>>>> >>> >> >> >>>>> I have the following files:
>>>> >>> >> >> >>>>> etc/gbrowse2/GBrowse.conf
>>>> >>> >> >> >>>>> var/www/gbrowse2/databases where I have the yeast_chr1+2
>>>> >>> >> >> >>>>> folder
>>>> >>> >> >> >>>>> with
>>>> >>> >> >> >>>>> my own data files
>>>> >>> >> >> >>>>> usr/lib/cgi-bin/gb2
>>>> >>> >> >> >>>>> var/lib/gbrowse2/databases/yeast_chr1+2 with other files
>>>> >>> >> >> >>>>>
>>>> >>> >> >> >>>>> but still the url http://localhost/cgi-bin/gbrowse2/yeast
>>>> >>> >> >> >>>>> shows
>>>> >>> >> >> >>>>> the
>>>> >>> >> >> >>>>> following url was not found on the server
>>>> >>> >> >> >>>>>
>>>> >>> >> >> >>>>> where is the cgi-bin mentioned in the url located when it
>>>> >>> >> >> >>>>> is
>>>> >>> >> >> >>>>> not
>>>> >>> >> >> >>>>> in
>>>> >>> >> >> >>>>> /var/www/
>>>> >>> >> >> >>>>>
>>>> >>> >> >> >>>>> On Wed, Sep 17, 2014 at 8:54 AM, umay kulsum
>>>> >>> >> >> >>>>> <[hidden email]>
>>>> >>> >> >> >>>>> wrote:
>>>> >>> >> >> >>>>>> Hi
>>>> >>> >> >> >>>>>> I have installed GBrowse using the command in ubuntu
>>>> >>> >> >> >>>>>> 14.04
>>>> >>> >> >> >>>>>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>>>> >>> >> >> >>>>>> but when I point my browser to
>>>> >>> >> >> >>>>>> http://localhost/cgi-bin/gbrowse2/yeast, it shows the
>>>> >>> >> >> >>>>>> following
>>>> >>> >> >> >>>>>> url
>>>> >>> >> >> >>>>>> is
>>>> >>> >> >> >>>>>> not found on this server..
>>>> >>> >> >> >>>>>> where is the cgi-bin mentioned in the url located when it
>>>> >>> >> >> >>>>>> is
>>>> >>> >> >> >>>>>> not
>>>> >>> >> >> >>>>>> in
>>>> >>> >> >> >>>>>> /var/www/
>>>> >>> >> >> >>>>>>
>>>> >>> >> >> >>>>>>> On Tue, Sep 16, 2014 at 2:28 AM, Scott Cain
>>>> >>> >> >> >>>>>>> <[hidden email]>
>>>> >>> >> >> >>>>>>> wrote:
>>>> >>> >> >> >>>>>>> Hi Umay,
>>>> >>> >> >> >>>>>>>
>>>> >>> >> >> >>>>>>> Can you please tell us what you done and where you think
>>>> >>> >> >> >>>>>>> the
>>>> >>> >> >> >>>>>>> process
>>>> >>> >> >> >>>>>>> has failed?  For instance, what do you see when you go
>>>> >>> >> >> >>>>>>> to
>>>> >>> >> >> >>>>>>> the
>>>> >>> >> >> >>>>>>> built in
>>>> >>> >> >> >>>>>>> sample yeast data set?
>>>> >>> >> >> >>>>>>>
>>>> >>> >> >> >>>>>>> Scott
>>>> >>> >> >> >>>>>>>
>>>> >>> >> >> >>>>>>> Sent from my iPhone
>>>> >>> >> >> >>>>>>>
>>>> >>> >> >> >>>>>>>> On Sep 11, 2014, at 11:41 PM, umay kulsum
>>>> >>> >> >> >>>>>>>> <[hidden email]>
>>>> >>> >> >> >>>>>>>> wrote:
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>> I have been trying to install and invoke GBrowse since
>>>> >>> >> >> >>>>>>>> a
>>>> >>> >> >> >>>>>>>> month
>>>> >>> >> >> >>>>>>>> but to
>>>> >>> >> >> >>>>>>>> no result....
>>>> >>> >> >> >>>>>>>> can someone help me regarding the installation process.
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>> ------------------------------------------------------------------------------
>>>> >>> >> >> >>>>>>>> Want excitement?
>>>> >>> >> >> >>>>>>>> Manually upgrade your production database.
>>>> >>> >> >> >>>>>>>> When you want reliability, choose Perforce
>>>> >>> >> >> >>>>>>>> Perforce version control. Predictably reliable.
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
>>>> >>> >> >> >>>>>>>> _______________________________________________
>>>> >>> >> >> >>>>>>>> Gmod-gbrowse mailing list
>>>> >>> >> >> >>>>>>>> [hidden email]
>>>> >>> >> >> >>>>>>>>
>>>> >>> >> >> >>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>> --
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>>
>>>> >>> >> >> >>>> ------------------------------------------------------------------------
>>>> >>> >> >> >>>> Scott Cain, Ph. D.                                   scott
>>>> >>> >> >> >>>> at
>>>> >>> >> >> >>>> scottcain dot
>>>> >>> >> >> >>>> net
>>>> >>> >> >> >>>> GMOD Coordinator (http://gmod.org/)
>>>> >>> >> >> >>>> <a href="tel:216-392-3087" value="+12163923087">216-392-3087
>>>> >>> >> >> >>>> Ontario Institute for Cancer Research
>>>> >>> >> >
>>>> >>> >> >
>>>> >>> >> >
>>>> >>> >> >
>>>> >>> >> > --
>>>> >>> >> >
>>>> >>> >> >
>>>> >>> >> > ------------------------------------------------------------------------
>>>> >>> >> > Scott Cain, Ph. D.                                   scott at
>>>> >>> >> > scottcain
>>>> >>> >> > dot
>>>> >>> >> > net
>>>> >>> >> > GMOD Coordinator (http://gmod.org/)
>>>> >>> >> > <a href="tel:216-392-3087" value="+12163923087">216-392-3087
>>>> >>> >> > Ontario Institute for Cancer Research
>>>> >>> >
>>>> >>> >
>>>> >>> >
>>>> >>> >
>>>> >>> > --
>>>> >>> >
>>>> >>> > ------------------------------------------------------------------------
>>>> >>> > Scott Cain, Ph. D.                                   scott at
>>>> >>> > scottcain
>>>> >>> > dot
>>>> >>> > net
>>>> >>> > GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
>>>> >>> > Ontario Institute for Cancer Research
>>>> >>
>>>> >>
>>>> >>
>>>> >>
>>>> >> --
>>>> >>
>>>> >> ------------------------------------------------------------------------
>>>> >> Scott Cain, Ph. D.                                   scott at scottcain
>>>> >> dot
>>>> >> net
>>>> >> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
>>>> >> Ontario Institute for Cancer Research
>>>
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot
>>> net
>>> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
>>> Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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