Gbrowse2.39 install problem

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Gbrowse2.39 install problem

ypfang
Dear all,
     I want to two Gbrowse2.39 to run in one linux machine. Can I install Gbrowse2.39 in two places seperately in one linux machine? I try it. But the second one overrite the first one. Thank you for your help!

Best wishes for you!

ypfang
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Re: Gbrowse2.39 install problem

Scott Cain
Hi ypfang,

I don't understand what you want to do.  Why would you want two
instances of GBrowse?  I would think you'd only want one and have more
than one configuration file for each data set, which would be the
typical usage.

Scott


On Fri, Aug 12, 2011 at 12:59 PM, Fang, Yaping <[hidden email]> wrote:

> Dear all,
>     I want to two Gbrowse2.39 to run in one linux machine. Can I install Gbrowse2.39 in two places seperately in one linux machine? I try it. But the second one overrite the first one. Thank you for your help!
>
> Best wishes for you!
>
> ypfang
> ------------------------------------------------------------------------------
> FREE DOWNLOAD - uberSVN with Social Coding for Subversion.
> Subversion made easy with a complete admin console. Easy
> to use, easy to manage, easy to install, easy to extend.
> Get a Free download of the new open ALM Subversion platform now.
> http://p.sf.net/sfu/wandisco-dev2dev
> _______________________________________________
> 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: Gbrowse2.39 install problem

ypfang
Dear Scott Cain,

     I have two projects and want to visulize them seperately (we do not want to the two project datas are display in one page). So I want to install two Gbrowse sperately. Can I have another way to do it?
Thank you for yur reply!

ypfang
________________________________________
From: Scott Cain [[hidden email]]
Sent: Friday, August 12, 2011 12:01 PM
To: Fang, Yaping
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem

Hi ypfang,

I don't understand what you want to do.  Why would you want two
instances of GBrowse?  I would think you'd only want one and have more
than one configuration file for each data set, which would be the
typical usage.

Scott


On Fri, Aug 12, 2011 at 12:59 PM, Fang, Yaping <[hidden email]> wrote:

> Dear all,
>     I want to two Gbrowse2.39 to run in one linux machine. Can I install Gbrowse2.39 in two places seperately in one linux machine? I try it. But the second one overrite the first one. Thank you for your help!
>
> Best wishes for you!
>
> ypfang
> ------------------------------------------------------------------------------
> FREE DOWNLOAD - uberSVN with Social Coding for Subversion.
> Subversion made easy with a complete admin console. Easy
> to use, easy to manage, easy to install, easy to extend.
> Get a Free download of the new open ALM Subversion platform now.
> http://p.sf.net/sfu/wandisco-dev2dev
> _______________________________________________
> 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: Gbrowse2.39 install problem

Todd Harris
Here's one approach that also let's you maintain completely separate copies of all library dependencies, too.

cd /path/to/installation_one
mkdir extlib ; cd extlib // or whatever
perl -Mlocal::lib=./
eval $(perl -Mlocal::lib=./)

cd /path/to/your/gbrowse/source
perl Build.PL
./Build reconfig
# Set paths as appropriate for your installation for cgi, html, databases, and temp
./Build install

Finally, config your HTTP server as appropriate for each installation for example using <VirtualHost> in apache or server { } in nginx.  You'll also need to specify your local library paths.

Todd


On Aug 12, 2011, at 11:22 AM, Fang, Yaping wrote:

> Dear Scott Cain,
>
>     I have two projects and want to visulize them seperately (we do not want to the two project datas are display in one page). So I want to install two Gbrowse sperately. Can I have another way to do it?
> Thank you for yur reply!
>
> ypfang
> ________________________________________
> From: Scott Cain [[hidden email]]
> Sent: Friday, August 12, 2011 12:01 PM
> To: Fang, Yaping
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem
>
> Hi ypfang,
>
> I don't understand what you want to do.  Why would you want two
> instances of GBrowse?  I would think you'd only want one and have more
> than one configuration file for each data set, which would be the
> typical usage.
>
> Scott
>
>
> On Fri, Aug 12, 2011 at 12:59 PM, Fang, Yaping <[hidden email]> wrote:
>> Dear all,
>>    I want to two Gbrowse2.39 to run in one linux machine. Can I install Gbrowse2.39 in two places seperately in one linux machine? I try it. But the second one overrite the first one. Thank you for your help!
>>
>> Best wishes for you!
>>
>> ypfang
>> ------------------------------------------------------------------------------
>> FREE DOWNLOAD - uberSVN with Social Coding for Subversion.
>> Subversion made easy with a complete admin console. Easy
>> to use, easy to manage, easy to install, easy to extend.
>> Get a Free download of the new open ALM Subversion platform now.
>> http://p.sf.net/sfu/wandisco-dev2dev
>> _______________________________________________
>> 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
> ------------------------------------------------------------------------------
> FREE DOWNLOAD - uberSVN with Social Coding for Subversion.
> Subversion made easy with a complete admin console. Easy
> to use, easy to manage, easy to install, easy to extend.
> Get a Free download of the new open ALM Subversion platform now.
> http://p.sf.net/sfu/wandisco-dev2dev
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


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Re: Gbrowse2.39 install problem

ypfang
Dear Todd Harris,
    Thank you for your words. Because I do not have the experience with apach configuration. Could you expain specificalyy how to config my HTTP server for each Gbrowse.
Suppose we install the Gbrowse in /var/www/html/example1 and /var/www/html/example2.

Best wishes for you!

________________________________________
From: Todd Harris [[hidden email]]
Sent: Friday, August 12, 2011 12:30 PM
To: Fang, Yaping
Cc: Scott Cain; [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem

Here's one approach that also let's you maintain completely separate copies of all library dependencies, too.

cd /path/to/installation_one
mkdir extlib ; cd extlib // or whatever
perl -Mlocal::lib=./
eval $(perl -Mlocal::lib=./)

cd /path/to/your/gbrowse/source
perl Build.PL
./Build reconfig
# Set paths as appropriate for your installation for cgi, html, databases, and temp
./Build install

Finally, config your HTTP server as appropriate for each installation for example using <VirtualHost> in apache or server { } in nginx.  You'll also need to specify your local library paths.

Todd


On Aug 12, 2011, at 11:22 AM, Fang, Yaping wrote:

> Dear Scott Cain,
>
>     I have two projects and want to visulize them seperately (we do not want to the two project datas are display in one page). So I want to install two Gbrowse sperately. Can I have another way to do it?
> Thank you for yur reply!
>
> ypfang
> ________________________________________
> From: Scott Cain [[hidden email]]
> Sent: Friday, August 12, 2011 12:01 PM
> To: Fang, Yaping
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem
>
> Hi ypfang,
>
> I don't understand what you want to do.  Why would you want two
> instances of GBrowse?  I would think you'd only want one and have more
> than one configuration file for each data set, which would be the
> typical usage.
>
> Scott
>
>
> On Fri, Aug 12, 2011 at 12:59 PM, Fang, Yaping <[hidden email]> wrote:
>> Dear all,
>>    I want to two Gbrowse2.39 to run in one linux machine. Can I install Gbrowse2.39 in two places seperately in one linux machine? I try it. But the second one overrite the first one. Thank you for your help!
>>
>> Best wishes for you!
>>
>> ypfang
>> ------------------------------------------------------------------------------
>> FREE DOWNLOAD - uberSVN with Social Coding for Subversion.
>> Subversion made easy with a complete admin console. Easy
>> to use, easy to manage, easy to install, easy to extend.
>> Get a Free download of the new open ALM Subversion platform now.
>> http://p.sf.net/sfu/wandisco-dev2dev
>> _______________________________________________
>> 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
> ------------------------------------------------------------------------------
> FREE DOWNLOAD - uberSVN with Social Coding for Subversion.
> Subversion made easy with a complete admin console. Easy
> to use, easy to manage, easy to install, easy to extend.
> Get a Free download of the new open ALM Subversion platform now.
> http://p.sf.net/sfu/wandisco-dev2dev
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
------------------------------------------------------------------------------
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to use, easy to manage, easy to install, easy to extend.
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Re: Gbrowse2.39 install problem

Todd Harris
Hi Fang -

The nuances of apache configuration are perhaps beyond the scope of this mailing list.  For example, are you looking to have both instances on the same host, under different host names/ports? Are you using a persistent environment like mod_perl or fastcgi?

Here are some suggestions.

Start with one GBrowse instance using local (*not* system level) library and installation paths as previously described.  Configure this as a VirtualHost using the sample apache configuration. You'll need the paths echoed by the local::lib command.  Once you get that instance working, you can install and configure your second instance exactly the same with alternative paths.

For multiple instances, you can maintain them as two separate name-based VirtualHosts ; as VirtualHosts listening on distinct ports; or as distinct <Directory> containers under a single VirtualHost.

Todd




On Aug 12, 2011, at 11:42 AM, Fang, Yaping wrote:

> Dear Todd Harris,
>    Thank you for your words. Because I do not have the experience with apach configuration. Could you expain specificalyy how to config my HTTP server for each Gbrowse.
> Suppose we install the Gbrowse in /var/www/html/example1 and /var/www/html/example2.
>
> Best wishes for you!
>
> ________________________________________
> From: Todd Harris [[hidden email]]
> Sent: Friday, August 12, 2011 12:30 PM
> To: Fang, Yaping
> Cc: Scott Cain; [hidden email]
> Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem
>
> Here's one approach that also let's you maintain completely separate copies of all library dependencies, too.
>
> cd /path/to/installation_one
> mkdir extlib ; cd extlib // or whatever
> perl -Mlocal::lib=./
> eval $(perl -Mlocal::lib=./)
>
> cd /path/to/your/gbrowse/source
> perl Build.PL
> ./Build reconfig
> # Set paths as appropriate for your installation for cgi, html, databases, and temp
> ./Build install
>
> Finally, config your HTTP server as appropriate for each installation for example using <VirtualHost> in apache or server { } in nginx.  You'll also need to specify your local library paths.
>
> Todd
>
>
> On Aug 12, 2011, at 11:22 AM, Fang, Yaping wrote:
>
>> Dear Scott Cain,
>>
>>    I have two projects and want to visulize them seperately (we do not want to the two project datas are display in one page). So I want to install two Gbrowse sperately. Can I have another way to do it?
>> Thank you for yur reply!
>>
>> ypfang
>> ________________________________________
>> From: Scott Cain [[hidden email]]
>> Sent: Friday, August 12, 2011 12:01 PM
>> To: Fang, Yaping
>> Cc: [hidden email]
>> Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem
>>
>> Hi ypfang,
>>
>> I don't understand what you want to do.  Why would you want two
>> instances of GBrowse?  I would think you'd only want one and have more
>> than one configuration file for each data set, which would be the
>> typical usage.
>>
>> Scott
>>
>>
>> On Fri, Aug 12, 2011 at 12:59 PM, Fang, Yaping <[hidden email]> wrote:
>>> Dear all,
>>>   I want to two Gbrowse2.39 to run in one linux machine. Can I install Gbrowse2.39 in two places seperately in one linux machine? I try it. But the second one overrite the first one. Thank you for your help!
>>>
>>> Best wishes for you!
>>>
>>> ypfang
>>> ------------------------------------------------------------------------------
>>> FREE DOWNLOAD - uberSVN with Social Coding for Subversion.
>>> Subversion made easy with a complete admin console. Easy
>>> to use, easy to manage, easy to install, easy to extend.
>>> Get a Free download of the new open ALM Subversion platform now.
>>> http://p.sf.net/sfu/wandisco-dev2dev
>>> _______________________________________________
>>> 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
>> ------------------------------------------------------------------------------
>> FREE DOWNLOAD - uberSVN with Social Coding for Subversion.
>> Subversion made easy with a complete admin console. Easy
>> to use, easy to manage, easy to install, easy to extend.
>> Get a Free download of the new open ALM Subversion platform now.
>> http://p.sf.net/sfu/wandisco-dev2dev
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
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Re: Gbrowse2.39 install problem

Scott Cain
In reply to this post by ypfang
Hi ypfang,

If you go to one of the installed sample yeast data sets, you'll see a
drop down box to let you choose which data set you want to look at.
Usually this is all people want or need in terms of keeping data
separate.  Other options include not showing that drop down box but
only allowing users to come to each instance via the appropriate url.
Password protected data sets and tracks are also an option.

Going the path that Todd suggested is also an option, but it is very
uncommon to need that sort of set up (though using local::lib is not a
bad idea for other reasons).  Going the more common route alleviates
the need for messing with the apache config.

Scott


On Fri, Aug 12, 2011 at 1:22 PM, Fang, Yaping <[hidden email]> wrote:

> Dear Scott Cain,
>
>     I have two projects and want to visulize them seperately (we do not want to the two project datas are display in one page). So I want to install two Gbrowse sperately. Can I have another way to do it?
> Thank you for yur reply!
>
> ypfang
> ________________________________________
> From: Scott Cain [[hidden email]]
> Sent: Friday, August 12, 2011 12:01 PM
> To: Fang, Yaping
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem
>
> Hi ypfang,
>
> I don't understand what you want to do.  Why would you want two
> instances of GBrowse?  I would think you'd only want one and have more
> than one configuration file for each data set, which would be the
> typical usage.
>
> Scott
>
>
> On Fri, Aug 12, 2011 at 12:59 PM, Fang, Yaping <[hidden email]> wrote:
>> Dear all,
>>     I want to two Gbrowse2.39 to run in one linux machine. Can I install Gbrowse2.39 in two places seperately in one linux machine? I try it. But the second one overrite the first one. Thank you for your help!
>>
>> Best wishes for you!
>>
>> ypfang
>> ------------------------------------------------------------------------------
>> FREE DOWNLOAD - uberSVN with Social Coding for Subversion.
>> Subversion made easy with a complete admin console. Easy
>> to use, easy to manage, easy to install, easy to extend.
>> Get a Free download of the new open ALM Subversion platform now.
>> http://p.sf.net/sfu/wandisco-dev2dev
>> _______________________________________________
>> 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: Gbrowse2.39 install problem

Todd Harris
Indeed, Scott's completely right and he proposes several simpler solutions.

My approach is for maintaining two completely independent GBrowse instances on a single server, perhaps even at unique host names.  If all you need is to have different datasets then you absolutely do not need more than one instance of GBrowse.

Even so, I still think it's appropriate to use local::lib and maintain GBrowse and libraries in a local path. I have over 40 versions of GBrowse installed now each with their own library dependencies.  It's trivial to roll back to an older version should the need arise.

Todd



On Aug 12, 2011, at 12:09 PM, Scott Cain wrote:

> Hi ypfang,
>
> If you go to one of the installed sample yeast data sets, you'll see a
> drop down box to let you choose which data set you want to look at.
> Usually this is all people want or need in terms of keeping data
> separate.  Other options include not showing that drop down box but
> only allowing users to come to each instance via the appropriate url.
> Password protected data sets and tracks are also an option.
>
> Going the path that Todd suggested is also an option, but it is very
> uncommon to need that sort of set up (though using local::lib is not a
> bad idea for other reasons).  Going the more common route alleviates
> the need for messing with the apache config.
>
> Scott
>
>
> On Fri, Aug 12, 2011 at 1:22 PM, Fang, Yaping <[hidden email]> wrote:
>> Dear Scott Cain,
>>
>>     I have two projects and want to visulize them seperately (we do not want to the two project datas are display in one page). So I want to install two Gbrowse sperately. Can I have another way to do it?
>> Thank you for yur reply!
>>
>> ypfang
>> ________________________________________
>> From: Scott Cain [[hidden email]]
>> Sent: Friday, August 12, 2011 12:01 PM
>> To: Fang, Yaping
>> Cc: [hidden email]
>> Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem
>>
>> Hi ypfang,
>>
>> I don't understand what you want to do.  Why would you want two
>> instances of GBrowse?  I would think you'd only want one and have more
>> than one configuration file for each data set, which would be the
>> typical usage.
>>
>> Scott
>>
>>
>> On Fri, Aug 12, 2011 at 12:59 PM, Fang, Yaping <[hidden email]> wrote:
>>> Dear all,
>>>     I want to two Gbrowse2.39 to run in one linux machine. Can I install Gbrowse2.39 in two places seperately in one linux machine? I try it. But the second one overrite the first one. Thank you for your help!
>>>
>>> Best wishes for you!
>>>
>>> ypfang
>>> ------------------------------------------------------------------------------
>>> FREE DOWNLOAD - uberSVN with Social Coding for Subversion.
>>> Subversion made easy with a complete admin console. Easy
>>> to use, easy to manage, easy to install, easy to extend.
>>> Get a Free download of the new open ALM Subversion platform now.
>>> http://p.sf.net/sfu/wandisco-dev2dev
>>> _______________________________________________
>>> 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
>
> ------------------------------------------------------------------------------
> FREE DOWNLOAD - uberSVN with Social Coding for Subversion.
> Subversion made easy with a complete admin console. Easy
> to use, easy to manage, easy to install, easy to extend.
> Get a Free download of the new open ALM Subversion platform now.
> http://p.sf.net/sfu/wandisco-dev2dev
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
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Re: Gbrowse2.39 install problem

ypfang
In reply to this post by Scott Cain
Dear Scott Cain and Todd Harris,
    Thank you for your suggestion. I think it is a simple way to use password to control display (Scott Cain suggested that Password protected data sets and tracks are also an option.).

To Scott Cain, Could you give a detail description how to do it?

Best wishes for all!

ypfang

________________________________________
From: Scott Cain [[hidden email]]
Sent: Friday, August 12, 2011 1:09 PM
To: Fang, Yaping
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem

Hi ypfang,

If you go to one of the installed sample yeast data sets, you'll see a
drop down box to let you choose which data set you want to look at.
Usually this is all people want or need in terms of keeping data
separate.  Other options include not showing that drop down box but
only allowing users to come to each instance via the appropriate url.
Password protected data sets and tracks are also an option.

Going the path that Todd suggested is also an option, but it is very
uncommon to need that sort of set up (though using local::lib is not a
bad idea for other reasons).  Going the more common route alleviates
the need for messing with the apache config.

Scott


On Fri, Aug 12, 2011 at 1:22 PM, Fang, Yaping <[hidden email]> wrote:

> Dear Scott Cain,
>
>     I have two projects and want to visulize them seperately (we do not want to the two project datas are display in one page). So I want to install two Gbrowse sperately. Can I have another way to do it?
> Thank you for yur reply!
>
> ypfang
> ________________________________________
> From: Scott Cain [[hidden email]]
> Sent: Friday, August 12, 2011 12:01 PM
> To: Fang, Yaping
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem
>
> Hi ypfang,
>
> I don't understand what you want to do.  Why would you want two
> instances of GBrowse?  I would think you'd only want one and have more
> than one configuration file for each data set, which would be the
> typical usage.
>
> Scott
>
>
> On Fri, Aug 12, 2011 at 12:59 PM, Fang, Yaping <[hidden email]> wrote:
>> Dear all,
>>     I want to two Gbrowse2.39 to run in one linux machine. Can I install Gbrowse2.39 in two places seperately in one linux machine? I try it. But the second one overrite the first one. Thank you for your help!
>>
>> Best wishes for you!
>>
>> ypfang
>> ------------------------------------------------------------------------------
>> FREE DOWNLOAD - uberSVN with Social Coding for Subversion.
>> Subversion made easy with a complete admin console. Easy
>> to use, easy to manage, easy to install, easy to extend.
>> Get a Free download of the new open ALM Subversion platform now.
>> http://p.sf.net/sfu/wandisco-dev2dev
>> _______________________________________________
>> 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
------------------------------------------------------------------------------
FREE DOWNLOAD - uberSVN with Social Coding for Subversion.
Subversion made easy with a complete admin console. Easy
to use, easy to manage, easy to install, easy to extend.
Get a Free download of the new open ALM Subversion platform now.
http://p.sf.net/sfu/wandisco-dev2dev
_______________________________________________
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Re: Gbrowse2.39 install problem

Scott Cain
Hi ypfang,

Since I don't know exactly what you want to do, the best thing for me
to do is to direct you to the wiki page covering this exact topic:

  http://gmod.org/wiki/GBrowse_Configuration/Authentication

Scott


On Fri, Aug 12, 2011 at 2:42 PM, Fang, Yaping <[hidden email]> wrote:

> Dear Scott Cain and Todd Harris,
>    Thank you for your suggestion. I think it is a simple way to use password to control display (Scott Cain suggested that Password protected data sets and tracks are also an option.).
>
> To Scott Cain, Could you give a detail description how to do it?
>
> Best wishes for all!
>
> ypfang
>
> ________________________________________
> From: Scott Cain [[hidden email]]
> Sent: Friday, August 12, 2011 1:09 PM
> To: Fang, Yaping
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem
>
> Hi ypfang,
>
> If you go to one of the installed sample yeast data sets, you'll see a
> drop down box to let you choose which data set you want to look at.
> Usually this is all people want or need in terms of keeping data
> separate.  Other options include not showing that drop down box but
> only allowing users to come to each instance via the appropriate url.
> Password protected data sets and tracks are also an option.
>
> Going the path that Todd suggested is also an option, but it is very
> uncommon to need that sort of set up (though using local::lib is not a
> bad idea for other reasons).  Going the more common route alleviates
> the need for messing with the apache config.
>
> Scott
>
>
> On Fri, Aug 12, 2011 at 1:22 PM, Fang, Yaping <[hidden email]> wrote:
>> Dear Scott Cain,
>>
>>     I have two projects and want to visulize them seperately (we do not want to the two project datas are display in one page). So I want to install two Gbrowse sperately. Can I have another way to do it?
>> Thank you for yur reply!
>>
>> ypfang
>> ________________________________________
>> From: Scott Cain [[hidden email]]
>> Sent: Friday, August 12, 2011 12:01 PM
>> To: Fang, Yaping
>> Cc: [hidden email]
>> Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem
>>
>> Hi ypfang,
>>
>> I don't understand what you want to do.  Why would you want two
>> instances of GBrowse?  I would think you'd only want one and have more
>> than one configuration file for each data set, which would be the
>> typical usage.
>>
>> Scott
>>
>>
>> On Fri, Aug 12, 2011 at 12:59 PM, Fang, Yaping <[hidden email]> wrote:
>>> Dear all,
>>>     I want to two Gbrowse2.39 to run in one linux machine. Can I install Gbrowse2.39 in two places seperately in one linux machine? I try it. But the second one overrite the first one. Thank you for your help!
>>>
>>> Best wishes for you!
>>>
>>> ypfang
>>> ------------------------------------------------------------------------------
>>> FREE DOWNLOAD - uberSVN with Social Coding for Subversion.
>>> Subversion made easy with a complete admin console. Easy
>>> to use, easy to manage, easy to install, easy to extend.
>>> Get a Free download of the new open ALM Subversion platform now.
>>> http://p.sf.net/sfu/wandisco-dev2dev
>>> _______________________________________________
>>> 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

------------------------------------------------------------------------------
FREE DOWNLOAD - uberSVN with Social Coding for Subversion.
Subversion made easy with a complete admin console. Easy
to use, easy to manage, easy to install, easy to extend.
Get a Free download of the new open ALM Subversion platform now.
http://p.sf.net/sfu/wandisco-dev2dev
_______________________________________________
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Re: Gbrowse2.39 install problem

ypfang
Dear Scott Cain and Todd Harris,
To Scott Cain,
    Thank you for your suggestion. After I read it. I think the Authentication method is not good enough to completely seperate two different projects.

To Todd Harris,
    Could you give me a example to configure the VirtualHost using the sample apache configuration. Suppose we want to install in /var/www/html/example1 and /var/www/html/example2.

Thank you!

Best wishes for all!

ypfang
________________________________________
From: Scott Cain [[hidden email]]
Sent: Friday, August 12, 2011 1:59 PM
To: Fang, Yaping
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem

Hi ypfang,

Since I don't know exactly what you want to do, the best thing for me
to do is to direct you to the wiki page covering this exact topic:

  http://gmod.org/wiki/GBrowse_Configuration/Authentication

Scott


On Fri, Aug 12, 2011 at 2:42 PM, Fang, Yaping <[hidden email]> wrote:

> Dear Scott Cain and Todd Harris,
>    Thank you for your suggestion. I think it is a simple way to use password to control display (Scott Cain suggested that Password protected data sets and tracks are also an option.).
>
> To Scott Cain, Could you give a detail description how to do it?
>
> Best wishes for all!
>
> ypfang
>
> ________________________________________
> From: Scott Cain [[hidden email]]
> Sent: Friday, August 12, 2011 1:09 PM
> To: Fang, Yaping
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem
>
> Hi ypfang,
>
> If you go to one of the installed sample yeast data sets, you'll see a
> drop down box to let you choose which data set you want to look at.
> Usually this is all people want or need in terms of keeping data
> separate.  Other options include not showing that drop down box but
> only allowing users to come to each instance via the appropriate url.
> Password protected data sets and tracks are also an option.
>
> Going the path that Todd suggested is also an option, but it is very
> uncommon to need that sort of set up (though using local::lib is not a
> bad idea for other reasons).  Going the more common route alleviates
> the need for messing with the apache config.
>
> Scott
>
>
> On Fri, Aug 12, 2011 at 1:22 PM, Fang, Yaping <[hidden email]> wrote:
>> Dear Scott Cain,
>>
>>     I have two projects and want to visulize them seperately (we do not want to the two project datas are display in one page). So I want to install two Gbrowse sperately. Can I have another way to do it?
>> Thank you for yur reply!
>>
>> ypfang
>> ________________________________________
>> From: Scott Cain [[hidden email]]
>> Sent: Friday, August 12, 2011 12:01 PM
>> To: Fang, Yaping
>> Cc: [hidden email]
>> Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem
>>
>> Hi ypfang,
>>
>> I don't understand what you want to do.  Why would you want two
>> instances of GBrowse?  I would think you'd only want one and have more
>> than one configuration file for each data set, which would be the
>> typical usage.
>>
>> Scott
>>
>>
>> On Fri, Aug 12, 2011 at 12:59 PM, Fang, Yaping <[hidden email]> wrote:
>>> Dear all,
>>>     I want to two Gbrowse2.39 to run in one linux machine. Can I install Gbrowse2.39 in two places seperately in one linux machine? I try it. But the second one overrite the first one. Thank you for your help!
>>>
>>> Best wishes for you!
>>>
>>> ypfang
>>> ------------------------------------------------------------------------------
>>> FREE DOWNLOAD - uberSVN with Social Coding for Subversion.
>>> Subversion made easy with a complete admin console. Easy
>>> to use, easy to manage, easy to install, easy to extend.
>>> Get a Free download of the new open ALM Subversion platform now.
>>> http://p.sf.net/sfu/wandisco-dev2dev
>>> _______________________________________________
>>> 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
------------------------------------------------------------------------------
FREE DOWNLOAD - uberSVN with Social Coding for Subversion.
Subversion made easy with a complete admin console. Easy
to use, easy to manage, easy to install, easy to extend.
Get a Free download of the new open ALM Subversion platform now.
http://p.sf.net/sfu/wandisco-dev2dev
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: Gbrowse2.39 install problem

Todd Harris
Hi Ypfang -

There are many, many different ways to do this.  Please describe in more detail what you are trying to accomplish.

Are these separate projects that will be responding to requests at different domain names? Do you want them all under the same domain name?

In either case, you should probably look up the documentation on VirtualHost in the httpd documentation.

Todd


On Aug 12, 2011, at 1:22 PM, Fang, Yaping wrote:

> Dear Scott Cain and Todd Harris,
> To Scott Cain,
>    Thank you for your suggestion. After I read it. I think the Authentication method is not good enough to completely seperate two different projects.
>
> To Todd Harris,
>    Could you give me a example to configure the VirtualHost using the sample apache configuration. Suppose we want to install in /var/www/html/example1 and /var/www/html/example2.
>
> Thank you!
>
> Best wishes for all!
>
> ypfang
> ________________________________________
> From: Scott Cain [[hidden email]]
> Sent: Friday, August 12, 2011 1:59 PM
> To: Fang, Yaping
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem
>
> Hi ypfang,
>
> Since I don't know exactly what you want to do, the best thing for me
> to do is to direct you to the wiki page covering this exact topic:
>
>  http://gmod.org/wiki/GBrowse_Configuration/Authentication
>
> Scott
>
>
> On Fri, Aug 12, 2011 at 2:42 PM, Fang, Yaping <[hidden email]> wrote:
>> Dear Scott Cain and Todd Harris,
>>   Thank you for your suggestion. I think it is a simple way to use password to control display (Scott Cain suggested that Password protected data sets and tracks are also an option.).
>>
>> To Scott Cain, Could you give a detail description how to do it?
>>
>> Best wishes for all!
>>
>> ypfang
>>
>> ________________________________________
>> From: Scott Cain [[hidden email]]
>> Sent: Friday, August 12, 2011 1:09 PM
>> To: Fang, Yaping
>> Cc: [hidden email]
>> Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem
>>
>> Hi ypfang,
>>
>> If you go to one of the installed sample yeast data sets, you'll see a
>> drop down box to let you choose which data set you want to look at.
>> Usually this is all people want or need in terms of keeping data
>> separate.  Other options include not showing that drop down box but
>> only allowing users to come to each instance via the appropriate url.
>> Password protected data sets and tracks are also an option.
>>
>> Going the path that Todd suggested is also an option, but it is very
>> uncommon to need that sort of set up (though using local::lib is not a
>> bad idea for other reasons).  Going the more common route alleviates
>> the need for messing with the apache config.
>>
>> Scott
>>
>>
>> On Fri, Aug 12, 2011 at 1:22 PM, Fang, Yaping <[hidden email]> wrote:
>>> Dear Scott Cain,
>>>
>>>    I have two projects and want to visulize them seperately (we do not want to the two project datas are display in one page). So I want to install two Gbrowse sperately. Can I have another way to do it?
>>> Thank you for yur reply!
>>>
>>> ypfang
>>> ________________________________________
>>> From: Scott Cain [[hidden email]]
>>> Sent: Friday, August 12, 2011 12:01 PM
>>> To: Fang, Yaping
>>> Cc: [hidden email]
>>> Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem
>>>
>>> Hi ypfang,
>>>
>>> I don't understand what you want to do.  Why would you want two
>>> instances of GBrowse?  I would think you'd only want one and have more
>>> than one configuration file for each data set, which would be the
>>> typical usage.
>>>
>>> Scott
>>>
>>>
>>> On Fri, Aug 12, 2011 at 12:59 PM, Fang, Yaping <[hidden email]> wrote:
>>>> Dear all,
>>>>    I want to two Gbrowse2.39 to run in one linux machine. Can I install Gbrowse2.39 in two places seperately in one linux machine? I try it. But the second one overrite the first one. Thank you for your help!
>>>>
>>>> Best wishes for you!
>>>>
>>>> ypfang
>>>> ------------------------------------------------------------------------------
>>>> FREE DOWNLOAD - uberSVN with Social Coding for Subversion.
>>>> Subversion made easy with a complete admin console. Easy
>>>> to use, easy to manage, easy to install, easy to extend.
>>>> Get a Free download of the new open ALM Subversion platform now.
>>>> http://p.sf.net/sfu/wandisco-dev2dev
>>>> _______________________________________________
>>>> 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


------------------------------------------------------------------------------
FREE DOWNLOAD - uberSVN with Social Coding for Subversion.
Subversion made easy with a complete admin console. Easy
to use, easy to manage, easy to install, easy to extend.
Get a Free download of the new open ALM Subversion platform now.
http://p.sf.net/sfu/wandisco-dev2dev
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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|

Re: Gbrowse2.39 install problem

ypfang
Dear Todd,
    I have configured the apache's configuration file but gbrowse do not work.
I add the following intems in the httpd.conf file:

ServerAdmin [hidden email]
Port 80
ServerName shark.abl.ku.edu
NameVirtualHost *:80
<VirtualHost *:80>
ServerName shark.abl.ku.edu
# Indexes + Directory Root.
DirectoryIndex index.html
DocumentRoot /var/www/html/
# CGI Directory
ScriptAlias /cgi-bin/ /var/www/cgi-bin/
<Location /cgi-bin>
    Options +ExecCGI
</Location>
</VirtualHost>

<VirtualHost *:80>
ServerName nhr.abl.ku.edu
# Indexes + Directory Root.
DirectoryIndex index.html
DocumentRoot /var/www/html/nhr/htdocs/
# CGI Directory
ScriptAlias /cgi-bin/ /var/www/cgi-bin/
<Location /cgi-bin>
    Options +ExecCGI
</Location>
</VirtualHost>

<VirtualHost *:80>
ServerName soumen.abl.ku.edu
# Indexes + Directory Root.
DirectoryIndex index.html
DocumentRoot /var/www/html/soumen/htdocs/
# CGI Directory
ScriptAlias /cgi-bin/ /var/www/cgi-bin/
<Location /cgi-bin>
    Options +ExecCGI
</Location>
</VirtualHost>

Could you give me a help? Thank you for your time!

Best wishes for you!

ypfang

________________________________________
From: Todd Harris [[hidden email]]
Sent: Friday, August 12, 2011 2:42 PM
To: Fang, Yaping
Cc: Scott Cain; [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem

Hi Ypfang -

There are many, many different ways to do this.  Please describe in more detail what you are trying to accomplish.

Are these separate projects that will be responding to requests at different domain names? Do you want them all under the same domain name?

In either case, you should probably look up the documentation on VirtualHost in the httpd documentation.

Todd


On Aug 12, 2011, at 1:22 PM, Fang, Yaping wrote:

> Dear Scott Cain and Todd Harris,
> To Scott Cain,
>    Thank you for your suggestion. After I read it. I think the Authentication method is not good enough to completely seperate two different projects.
>
> To Todd Harris,
>    Could you give me a example to configure the VirtualHost using the sample apache configuration. Suppose we want to install in /var/www/html/example1 and /var/www/html/example2.
>
> Thank you!
>
> Best wishes for all!
>
> ypfang
> ________________________________________
> From: Scott Cain [[hidden email]]
> Sent: Friday, August 12, 2011 1:59 PM
> To: Fang, Yaping
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem
>
> Hi ypfang,
>
> Since I don't know exactly what you want to do, the best thing for me
> to do is to direct you to the wiki page covering this exact topic:
>
>  http://gmod.org/wiki/GBrowse_Configuration/Authentication
>
> Scott
>
>
> On Fri, Aug 12, 2011 at 2:42 PM, Fang, Yaping <[hidden email]> wrote:
>> Dear Scott Cain and Todd Harris,
>>   Thank you for your suggestion. I think it is a simple way to use password to control display (Scott Cain suggested that Password protected data sets and tracks are also an option.).
>>
>> To Scott Cain, Could you give a detail description how to do it?
>>
>> Best wishes for all!
>>
>> ypfang
>>
>> ________________________________________
>> From: Scott Cain [[hidden email]]
>> Sent: Friday, August 12, 2011 1:09 PM
>> To: Fang, Yaping
>> Cc: [hidden email]
>> Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem
>>
>> Hi ypfang,
>>
>> If you go to one of the installed sample yeast data sets, you'll see a
>> drop down box to let you choose which data set you want to look at.
>> Usually this is all people want or need in terms of keeping data
>> separate.  Other options include not showing that drop down box but
>> only allowing users to come to each instance via the appropriate url.
>> Password protected data sets and tracks are also an option.
>>
>> Going the path that Todd suggested is also an option, but it is very
>> uncommon to need that sort of set up (though using local::lib is not a
>> bad idea for other reasons).  Going the more common route alleviates
>> the need for messing with the apache config.
>>
>> Scott
>>
>>
>> On Fri, Aug 12, 2011 at 1:22 PM, Fang, Yaping <[hidden email]> wrote:
>>> Dear Scott Cain,
>>>
>>>    I have two projects and want to visulize them seperately (we do not want to the two project datas are display in one page). So I want to install two Gbrowse sperately. Can I have another way to do it?
>>> Thank you for yur reply!
>>>
>>> ypfang
>>> ________________________________________
>>> From: Scott Cain [[hidden email]]
>>> Sent: Friday, August 12, 2011 12:01 PM
>>> To: Fang, Yaping
>>> Cc: [hidden email]
>>> Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem
>>>
>>> Hi ypfang,
>>>
>>> I don't understand what you want to do.  Why would you want two
>>> instances of GBrowse?  I would think you'd only want one and have more
>>> than one configuration file for each data set, which would be the
>>> typical usage.
>>>
>>> Scott
>>>
>>>
>>> On Fri, Aug 12, 2011 at 12:59 PM, Fang, Yaping <[hidden email]> wrote:
>>>> Dear all,
>>>>    I want to two Gbrowse2.39 to run in one linux machine. Can I install Gbrowse2.39 in two places seperately in one linux machine? I try it. But the second one overrite the first one. Thank you for your help!
>>>>
>>>> Best wishes for you!
>>>>
>>>> ypfang
>>>> ------------------------------------------------------------------------------
>>>> FREE DOWNLOAD - uberSVN with Social Coding for Subversion.
>>>> Subversion made easy with a complete admin console. Easy
>>>> to use, easy to manage, easy to install, easy to extend.
>>>> Get a Free download of the new open ALM Subversion platform now.
>>>> http://p.sf.net/sfu/wandisco-dev2dev
>>>> _______________________________________________
>>>> 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
------------------------------------------------------------------------------
FREE DOWNLOAD - uberSVN with Social Coding for Subversion.
Subversion made easy with a complete admin console. Easy
to use, easy to manage, easy to install, easy to extend.
Get a Free download of the new open ALM Subversion platform now.
http://p.sf.net/sfu/wandisco-dev2dev
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: Gbrowse2.39 install problem

ypfang
In reply to this post by Todd Harris
Dear Todd Harris,
    Thank you for your help! Now I have install Gbrowse seperately. They are installed in /var/www/html/nhr and /var/www/htm/soumen sperately. And I added the following part in the end of httpd.conf file:

NameVirtualHost *:8880
NameVirtualHost *:8881

<VirtualHost *:8880>
<Directory "/var/www/html/nhr/htdocs">
   Options FollowSymLinks
   AllowOverride None
   Order allow,deny
   Allow from all
</Directory>
   ServerName nhr.abl.ku.edu
   DocumentRoot /var/www/html/nhr/htdocs
</VirtualHost>

<VirtualHost *:8881>
<VirtualHost *:8881>
<Directory "/var/www/html/soumen/htdocs">
   Options FollowSymLinks
   AllowOverride None
   Order allow,deny
   Allow from all
</Directory>
    ServerName soumen.abl.ku.edu
    DocumentRoot /var/www/html/soumen/htdocs
</VirtualHost>


But the the two sites do not work. Then I checked and found that there are two symbolic links in the apache directory (/usr/local/apache/) that may influence the file directions.
The links are htdocs -> /var/www/html  and  cgi-bin -> /var/www/cgi-bin.
Now I am really confusing about how to solve it? Could you give me a help? Thank you for your time!

Best wishes for you!

ypfang

________________________________________
From: Todd Harris [[hidden email]]
Sent: Friday, August 12, 2011 2:42 PM
To: Fang, Yaping
Cc: Scott Cain; [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem

Hi Ypfang -

There are many, many different ways to do this.  Please describe in more detail what you are trying to accomplish.

Are these separate projects that will be responding to requests at different domain names? Do you want them all under the same domain name?

In either case, you should probably look up the documentation on VirtualHost in the httpd documentation.

Todd


On Aug 12, 2011, at 1:22 PM, Fang, Yaping wrote:

> Dear Scott Cain and Todd Harris,
> To Scott Cain,
>    Thank you for your suggestion. After I read it. I think the Authentication method is not good enough to completely seperate two different projects.
>
> To Todd Harris,
>    Could you give me a example to configure the VirtualHost using the sample apache configuration. Suppose we want to install in /var/www/html/example1 and /var/www/html/example2.
>
> Thank you!
>
> Best wishes for all!
>
> ypfang
> ________________________________________
> From: Scott Cain [[hidden email]]
> Sent: Friday, August 12, 2011 1:59 PM
> To: Fang, Yaping
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem
>
> Hi ypfang,
>
> Since I don't know exactly what you want to do, the best thing for me
> to do is to direct you to the wiki page covering this exact topic:
>
>  http://gmod.org/wiki/GBrowse_Configuration/Authentication
>
> Scott
>
>
> On Fri, Aug 12, 2011 at 2:42 PM, Fang, Yaping <[hidden email]> wrote:
>> Dear Scott Cain and Todd Harris,
>>   Thank you for your suggestion. I think it is a simple way to use password to control display (Scott Cain suggested that Password protected data sets and tracks are also an option.).
>>
>> To Scott Cain, Could you give a detail description how to do it?
>>
>> Best wishes for all!
>>
>> ypfang
>>
>> ________________________________________
>> From: Scott Cain [[hidden email]]
>> Sent: Friday, August 12, 2011 1:09 PM
>> To: Fang, Yaping
>> Cc: [hidden email]
>> Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem
>>
>> Hi ypfang,
>>
>> If you go to one of the installed sample yeast data sets, you'll see a
>> drop down box to let you choose which data set you want to look at.
>> Usually this is all people want or need in terms of keeping data
>> separate.  Other options include not showing that drop down box but
>> only allowing users to come to each instance via the appropriate url.
>> Password protected data sets and tracks are also an option.
>>
>> Going the path that Todd suggested is also an option, but it is very
>> uncommon to need that sort of set up (though using local::lib is not a
>> bad idea for other reasons).  Going the more common route alleviates
>> the need for messing with the apache config.
>>
>> Scott
>>
>>
>> On Fri, Aug 12, 2011 at 1:22 PM, Fang, Yaping <[hidden email]> wrote:
>>> Dear Scott Cain,
>>>
>>>    I have two projects and want to visulize them seperately (we do not want to the two project datas are display in one page). So I want to install two Gbrowse sperately. Can I have another way to do it?
>>> Thank you for yur reply!
>>>
>>> ypfang
>>> ________________________________________
>>> From: Scott Cain [[hidden email]]
>>> Sent: Friday, August 12, 2011 12:01 PM
>>> To: Fang, Yaping
>>> Cc: [hidden email]
>>> Subject: Re: [Gmod-gbrowse] Gbrowse2.39 install problem
>>>
>>> Hi ypfang,
>>>
>>> I don't understand what you want to do.  Why would you want two
>>> instances of GBrowse?  I would think you'd only want one and have more
>>> than one configuration file for each data set, which would be the
>>> typical usage.
>>>
>>> Scott
>>>
>>>
>>> On Fri, Aug 12, 2011 at 12:59 PM, Fang, Yaping <[hidden email]> wrote:
>>>> Dear all,
>>>>    I want to two Gbrowse2.39 to run in one linux machine. Can I install Gbrowse2.39 in two places seperately in one linux machine? I try it. But the second one overrite the first one. Thank you for your help!
>>>>
>>>> Best wishes for you!
>>>>
>>>> ypfang
>>>> ------------------------------------------------------------------------------
>>>> FREE DOWNLOAD - uberSVN with Social Coding for Subversion.
>>>> Subversion made easy with a complete admin console. Easy
>>>> to use, easy to manage, easy to install, easy to extend.
>>>> Get a Free download of the new open ALM Subversion platform now.
>>>> http://p.sf.net/sfu/wandisco-dev2dev
>>>> _______________________________________________
>>>> 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: Gbrowse2.39 install problem

JINGJING JIN-2
I have read your post on GMOD. I also have the same problem.

After reading your posters, I still have some problems.

How can you install two different separately.

I am fear that the two install will overrite the first one.

During the installation, do I just need to change the folder of these:

GBrowse documentation, stylesheets and in-memory databases.
    /var/www/gbrowse2

GBrowse configuration files
    /etc/gbrowse2/GBrowse.conf

Preinstalled sample database(s)
    /var/lib/gbrowse2/databases

GBrowse CGI (web) scripts  

        /usr/lib/cgi-bin/gb2/gbrowse
        /usr/lib/cgi-bin/gb2/gbrowse_img
        /usr/lib/cgi-bin/gb2/gbrowse_details

Temporary directories for cached images and sessions.
    /tmp/gbrowse2

Or just the first three folders?

In addition, after that do I just need to do like your description:

And I added the following part in the end of httpd.conf file:

NameVirtualHost *:8880
NameVirtualHost *:8881

<VirtualHost *:8880>
<Directory "/var/www/html/nhr/htdocs">
   Options FollowSymLinks
   AllowOverride None
   Order allow,deny
   Allow from all
</Directory>
   ServerName nhr.abl.ku.edu
   DocumentRoot /var/www/html/nhr/htdocs
</VirtualHost>

<VirtualHost *:8881>
<VirtualHost *:8881>
<Directory "/var/www/html/soumen/htdocs">
   Options FollowSymLinks
   AllowOverride None
   Order allow,deny
   Allow from all
</Directory>
    ServerName soumen.abl.ku.edu
    DocumentRoot /var/www/html/soumen/htdocs
</VirtualHost>

This file is for apahce configuration?

Thanks!

jingjing

--
View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/Gbrowse2-39-install-problem-tp4694012p4890169.html
Sent from the gmod-gbrowse mailing list archive at Nabble.com.

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Re: Gbrowse2.39 install problem

Todd Harris
To have two completely distinct installations running on the same server:

1. Set each and every path to a distinct location via "Build reconfig".

2. You will also want to install Perl libraries to distinct paths. One easy way to do this is using local::lib.

3. Add your library paths to your apache virtual host containers.  This will vary depending on how you are running gbrowse (vanilla CGI, Fast CGI, etc).

Notes:

The way you have your apache configuration set up -- and assuming you don't have a proxy -- users will have to specify the port (for example  nhr.abl.ku.edu:8880).  Is this what you want?  It's also broken - you open the VirtualHost *:8881 container twice.

Todd



On Oct 10, 2011, at 8:05 PM, jjjscuedu wrote:

> I have read your post on GMOD. I also have the same problem.
>
> After reading your posters, I still have some problems.
>
> How can you install two different separately.
>
> I am fear that the two install will overrite the first one.
>
> During the installation, do I just need to change the folder of these:
>
> GBrowse documentation, stylesheets and in-memory databases.
>    /var/www/gbrowse2
>
> GBrowse configuration files
>    /etc/gbrowse2/GBrowse.conf
>
> Preinstalled sample database(s)
>    /var/lib/gbrowse2/databases
>
> GBrowse CGI (web) scripts  
>
>        /usr/lib/cgi-bin/gb2/gbrowse
>        /usr/lib/cgi-bin/gb2/gbrowse_img
>        /usr/lib/cgi-bin/gb2/gbrowse_details
>
> Temporary directories for cached images and sessions.
>    /tmp/gbrowse2
>
> Or just the first three folders?
>
> In addition, after that do I just need to do like your description:
>
> And I added the following part in the end of httpd.conf file:
>
> NameVirtualHost *:8880
> NameVirtualHost *:8881
>
> <VirtualHost *:8880>
> <Directory "/var/www/html/nhr/htdocs">
>   Options FollowSymLinks
>   AllowOverride None
>   Order allow,deny
>   Allow from all
> </Directory>
>   ServerName nhr.abl.ku.edu
>   DocumentRoot /var/www/html/nhr/htdocs
> </VirtualHost>
>
> <VirtualHost *:8881>
> <VirtualHost *:8881>
> <Directory "/var/www/html/soumen/htdocs">
>   Options FollowSymLinks
>   AllowOverride None
>   Order allow,deny
>   Allow from all
> </Directory>
>    ServerName soumen.abl.ku.edu
>    DocumentRoot /var/www/html/soumen/htdocs
> </VirtualHost>
>
> This file is for apahce configuration?
>
> Thanks!
>
> jingjing
>
> --
> View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/Gbrowse2-39-install-problem-tp4694012p4890169.html
> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2d-oct
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct
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Are html inserts working from config file?

Victor-2
Hi,

I tried to use HTML inserts in GBrowse2 (html1, html2 and so on to
html6) and just cannot make them work using just config file. But
they are listed in GBrowse2 howto and look not different from GBrowse1..

Can I have some confirmation that html inserts are really working in GBrowse2?

Using them to inject my javascript code into browser window, to be
used by glyphs..

Thanks in advance,

Victor


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Re: Are html inserts working from config file?

vstrelet

On Monday, September 10, 2012 02:13:43 PM Victor wrote:

> I tried to use HTML inserts in GBrowse2 (html1, html2 and so on to

> html6) and just cannot make them work using just config file. But

> they are listed in GBrowse2 howto and look not different from GBrowse1..

>

> Can I have some confirmation that html inserts are really working in

> GBrowse2?

 

Hmm, header not working too..

But don't need to have answer - I debugged the thing

and found that several subroutines in HTML.pm are not

working right. Checking for things in wrong, non-existing

locations.

 

Illustrating on sub HTML::render_user_header (in GBrowse v 2.39)

(and sorry, if it is already fixed in latest version)

 

Currently, that sub has:

 

sub render_user_header {

my $self = shift;

my $settings = $self->state;

return '' unless $settings->{head};

my $a= $self->data_source->global_setting('header');

return $a->(@_) if ref $a eq 'CODE';

return $a || '';

}

 

But actual code which will do (and does, I checked)

the trick should be:

 

sub render_user_header {

my $self = shift;

my $settings = $self->state;

my $a= $self->data_source->{config}->{'TRACK DEFAULTS'}->{header};

return $a->(@_) if ref $a eq 'CODE';

return $a || '';

}

 


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