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Not Found

navillusol
Hello, I have been having issues with invoking anything but the tutorial
databases that come with gbrowse2. I have my own data that I wish to view
however after creating the necessary .conf files I still have no success.

So i decided to make an exact duplicate of the example volvox. I made a
seperate .conf file using the remarks gff3. I edited the main gbrowse.cof
file to allow access, I created a database in the correct path for this conf
file and placed the necessary folder in it. So everything is the exact same
and still it does not work. I get an error saying not found when trying to
invoke it.

the permissions on the databases are as follows:

drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 admin_uploads
*drwxrwxr-x 2 www-data www-data  4096 Aug 11 15:43 duplicate_volvox*
drwxrwxr-x 5 www-data www-data  4096 Jul 17 14:49 gbrowse_syn
drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 ideograms
drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 pop_demo
-rwxrwxr-x 1 www-data www-data 16384 Aug 11 17:02 users.sqlite
drwxrwxr-x 2 www-data www-data  4096 Aug 11 14:57 volvox
drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 yeast_chr1+2
drwxrwxr-x 2 www-data www-data  4096 Jul 17 15:21 yeast_scaffolds

I invoke the data using http://localhost/cgi-bin/gb2/gbrowse/volvoxDouble/
and the following is an image of the result (it is the same for all except
the tutorial files)

<http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712696/22.png>



I just do not understand what the problem is!? any help would be much
appreciated.






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Re: Not Found

Scott Cain
Hi Liam,

The most useful things for helping us help you debug this are the GBrowse.conf file, the dataset conf file, the top several lines of the GFF file and the last several lines of the apache error log.  The "not found" problem is pretty common, assuming you are referring to the case when you get a GBrowse page but you get in large read letters "Not found"; this is usually a GFF problem.  There are also file not found issues which are not uncommon and would be best be debugged with the combination of the config files and the apache error log (this usually happens when GBrowse is looking in one place for a file but you've put it somewhere else).

Scott



On Mon, Aug 11, 2014 at 12:28 PM, navillusol <[hidden email]> wrote:
Hello, I have been having issues with invoking anything but the tutorial
databases that come with gbrowse2. I have my own data that I wish to view
however after creating the necessary .conf files I still have no success.

So i decided to make an exact duplicate of the example volvox. I made a
seperate .conf file using the remarks gff3. I edited the main gbrowse.cof
file to allow access, I created a database in the correct path for this conf
file and placed the necessary folder in it. So everything is the exact same
and still it does not work. I get an error saying not found when trying to
invoke it.

the permissions on the databases are as follows:

drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 admin_uploads
*drwxrwxr-x 2 www-data www-data  4096 Aug 11 15:43 duplicate_volvox*
drwxrwxr-x 5 www-data www-data  4096 Jul 17 14:49 gbrowse_syn
drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 ideograms
drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 pop_demo
-rwxrwxr-x 1 www-data www-data 16384 Aug 11 17:02 users.sqlite
drwxrwxr-x 2 www-data www-data  4096 Aug 11 14:57 volvox
drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 yeast_chr1+2
drwxrwxr-x 2 www-data www-data  4096 Jul 17 15:21 yeast_scaffolds

I invoke the data using http://localhost/cgi-bin/gb2/gbrowse/volvoxDouble/
and the following is an image of the result (it is the same for all except
the tutorial files)

<http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712696/22.png>



I just do not understand what the problem is!? any help would be much
appreciated.






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Ontario Institute for Cancer Research

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Re: Not Found

Matthew Johnson
Hi Scott and Liam,

I have had the same issues with the "Not Found" after loading my data
and conf file.  I thought it was an error with the gff format so cut
it to about ten lines and made sure followed the format outlined at
http://www.sequenceontology.org/gff3.shtml. but still got the "Not
found".  Scott recommended downgrading a certain module but with my
little knowledge on dealing with CPAN, perl modules and linux I got
stuck.  I then tried the already configured GBrowse on the virtual
machine, thinking maybe I didn't have a clean install on my own
machine but still got the same "Not found" error.  I have since gave
it a break but I have recently started trying again from scratch.
Please keep my posted about your endeavours with this error.

Thanks,
Matt

On Mon, Aug 11, 2014 at 1:09 PM, Scott Cain <[hidden email]> wrote:

> Hi Liam,
>
> The most useful things for helping us help you debug this are the
> GBrowse.conf file, the dataset conf file, the top several lines of the GFF
> file and the last several lines of the apache error log.  The "not found"
> problem is pretty common, assuming you are referring to the case when you
> get a GBrowse page but you get in large read letters "Not found"; this is
> usually a GFF problem.  There are also file not found issues which are not
> uncommon and would be best be debugged with the combination of the config
> files and the apache error log (this usually happens when GBrowse is looking
> in one place for a file but you've put it somewhere else).
>
> Scott
>
>
>
> On Mon, Aug 11, 2014 at 12:28 PM, navillusol <[hidden email]>
> wrote:
>>
>> Hello, I have been having issues with invoking anything but the tutorial
>> databases that come with gbrowse2. I have my own data that I wish to view
>> however after creating the necessary .conf files I still have no success.
>>
>> So i decided to make an exact duplicate of the example volvox. I made a
>> seperate .conf file using the remarks gff3. I edited the main gbrowse.cof
>> file to allow access, I created a database in the correct path for this
>> conf
>> file and placed the necessary folder in it. So everything is the exact
>> same
>> and still it does not work. I get an error saying not found when trying to
>> invoke it.
>>
>> the permissions on the databases are as follows:
>>
>> drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 admin_uploads
>> *drwxrwxr-x 2 www-data www-data  4096 Aug 11 15:43 duplicate_volvox*
>> drwxrwxr-x 5 www-data www-data  4096 Jul 17 14:49 gbrowse_syn
>> drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 ideograms
>> drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 pop_demo
>> -rwxrwxr-x 1 www-data www-data 16384 Aug 11 17:02 users.sqlite
>> drwxrwxr-x 2 www-data www-data  4096 Aug 11 14:57 volvox
>> drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 yeast_chr1+2
>> drwxrwxr-x 2 www-data www-data  4096 Jul 17 15:21 yeast_scaffolds
>>
>> I invoke the data using http://localhost/cgi-bin/gb2/gbrowse/volvoxDouble/
>> and the following is an image of the result (it is the same for all except
>> the tutorial files)
>>
>>
>> <http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712696/22.png>
>>
>>
>>
>> I just do not understand what the problem is!? any help would be much
>> appreciated.
>>
>>
>>
>>
>>
>>
>> --
>> View this message in context:
>> http://generic-model-organism-system-database.450254.n5.nabble.com/Not-Found-tp5712696.html
>> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>>
>>
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> 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
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Gmod-gbrowse mailing list
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> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

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Re: Not Found

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

Please cc your responses to the GBrowse mailing list so other people can help and the resolution can be archived.

I don't see anything wrong with the GFF file itself (which isn't surprising since it's exactly the first gff file from the tutorial), though I wonder what it's really named: does it have a .gff or .gff3 appended to the end of the filename?  The underlying BioPerl code almost certainly requires that.

The only other thing I see that's not quite what I would expect is that the snippet of error log you sent references the volvox directory no the sample directory that you want to use.  When you try to load the sample database, does that cause anything to be written to the error log?

Scott



On Thu, Aug 14, 2014 at 12:03 PM, Liam O'Sullivan <[hidden email]> wrote:
Hello Scott,

Yup that is the exact error that I have, there is no issue with the pre-made datasets that were provided with installation. They work perfectly and can be modified.

Attached is my Gbrowse.conf file, the dataset conf file, the GFF3 and the end of the apache error file. 

I have simply made a copy of the volvox conf and GFF3 to ensure that it was not an error with my own conf/GFF3. The files are all located in the correct directories with the required permissions.

Thanks for the help Scott,
Regards,
Liam


On Mon, Aug 11, 2014 at 7:09 PM, Scott Cain <[hidden email]> wrote:
Hi Liam,

The most useful things for helping us help you debug this are the GBrowse.conf file, the dataset conf file, the top several lines of the GFF file and the last several lines of the apache error log.  The "not found" problem is pretty common, assuming you are referring to the case when you get a GBrowse page but you get in large read letters "Not found"; this is usually a GFF problem.  There are also file not found issues which are not uncommon and would be best be debugged with the combination of the config files and the apache error log (this usually happens when GBrowse is looking in one place for a file but you've put it somewhere else).

Scott



On Mon, Aug 11, 2014 at 12:28 PM, navillusol <[hidden email]> wrote:
Hello, I have been having issues with invoking anything but the tutorial
databases that come with gbrowse2. I have my own data that I wish to view
however after creating the necessary .conf files I still have no success.

So i decided to make an exact duplicate of the example volvox. I made a
seperate .conf file using the remarks gff3. I edited the main gbrowse.cof
file to allow access, I created a database in the correct path for this conf
file and placed the necessary folder in it. So everything is the exact same
and still it does not work. I get an error saying not found when trying to
invoke it.

the permissions on the databases are as follows:

drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 admin_uploads
*drwxrwxr-x 2 www-data www-data  4096 Aug 11 15:43 duplicate_volvox*
drwxrwxr-x 5 www-data www-data  4096 Jul 17 14:49 gbrowse_syn
drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 ideograms
drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 pop_demo
-rwxrwxr-x 1 www-data www-data 16384 Aug 11 17:02 users.sqlite
drwxrwxr-x 2 www-data www-data  4096 Aug 11 14:57 volvox
drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 yeast_chr1+2
drwxrwxr-x 2 www-data www-data  4096 Jul 17 15:21 yeast_scaffolds

I invoke the data using http://localhost/cgi-bin/gb2/gbrowse/volvoxDouble/
and the following is an image of the result (it is the same for all except
the tutorial files)

<http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712696/22.png>



I just do not understand what the problem is!? any help would be much
appreciated.






--
View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/Not-Found-tp5712696.html
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">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: Not Found

navillusol
Sorry for not cc-ing Scott, you were spot on that is exactly what the problem was (no .gff3 after the filename). I am so sorry what a trivial error to make. The sample database that I created is working perfectly now also! :-)

No nothing in the error log refers to the sample database, but I do find errors for volvox which is strange considering it is working perfectly!?

Thanks again for the help Scott, I really appreciate it!

Regards,
Liam


On Thu, Aug 14, 2014 at 5:21 PM, Scott Cain <[hidden email]> wrote:
Hi Liam,

Please cc your responses to the GBrowse mailing list so other people can help and the resolution can be archived.

I don't see anything wrong with the GFF file itself (which isn't surprising since it's exactly the first gff file from the tutorial), though I wonder what it's really named: does it have a .gff or .gff3 appended to the end of the filename?  The underlying BioPerl code almost certainly requires that.

The only other thing I see that's not quite what I would expect is that the snippet of error log you sent references the volvox directory no the sample directory that you want to use.  When you try to load the sample database, does that cause anything to be written to the error log?

Scott



On Thu, Aug 14, 2014 at 12:03 PM, Liam O'Sullivan <[hidden email]> wrote:
Hello Scott,

Yup that is the exact error that I have, there is no issue with the pre-made datasets that were provided with installation. They work perfectly and can be modified.

Attached is my Gbrowse.conf file, the dataset conf file, the GFF3 and the end of the apache error file. 

I have simply made a copy of the volvox conf and GFF3 to ensure that it was not an error with my own conf/GFF3. The files are all located in the correct directories with the required permissions.

Thanks for the help Scott,
Regards,
Liam


On Mon, Aug 11, 2014 at 7:09 PM, Scott Cain <[hidden email]> wrote:
Hi Liam,

The most useful things for helping us help you debug this are the GBrowse.conf file, the dataset conf file, the top several lines of the GFF file and the last several lines of the apache error log.  The "not found" problem is pretty common, assuming you are referring to the case when you get a GBrowse page but you get in large read letters "Not found"; this is usually a GFF problem.  There are also file not found issues which are not uncommon and would be best be debugged with the combination of the config files and the apache error log (this usually happens when GBrowse is looking in one place for a file but you've put it somewhere else).

Scott



On Mon, Aug 11, 2014 at 12:28 PM, navillusol <[hidden email]> wrote:
Hello, I have been having issues with invoking anything but the tutorial
databases that come with gbrowse2. I have my own data that I wish to view
however after creating the necessary .conf files I still have no success.

So i decided to make an exact duplicate of the example volvox. I made a
seperate .conf file using the remarks gff3. I edited the main gbrowse.cof
file to allow access, I created a database in the correct path for this conf
file and placed the necessary folder in it. So everything is the exact same
and still it does not work. I get an error saying not found when trying to
invoke it.

the permissions on the databases are as follows:

drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 admin_uploads
*drwxrwxr-x 2 www-data www-data  4096 Aug 11 15:43 duplicate_volvox*
drwxrwxr-x 5 www-data www-data  4096 Jul 17 14:49 gbrowse_syn
drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 ideograms
drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 pop_demo
-rwxrwxr-x 1 www-data www-data 16384 Aug 11 17:02 users.sqlite
drwxrwxr-x 2 www-data www-data  4096 Aug 11 14:57 volvox
drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 yeast_chr1+2
drwxrwxr-x 2 www-data www-data  4096 Jul 17 15:21 yeast_scaffolds

I invoke the data using http://localhost/cgi-bin/gb2/gbrowse/volvoxDouble/
and the following is an image of the result (it is the same for all except
the tutorial files)

<http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712696/22.png>



I just do not understand what the problem is!? any help would be much
appreciated.






--
View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/Not-Found-tp5712696.html
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">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" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Re: Not Found

Scott Cain
Perhaps they are old errors for which you've already fixed the problem?  It's hard to say since your apache instance isn't configured to record the date and time at which the problem occurred.  As long as it's working now, I wouldn't worry too much about it.  Glad you got it sorted.

Scott



On Thu, Aug 14, 2014 at 12:37 PM, Liam O'Sullivan <[hidden email]> wrote:
Sorry for not cc-ing Scott, you were spot on that is exactly what the problem was (no .gff3 after the filename). I am so sorry what a trivial error to make. The sample database that I created is working perfectly now also! :-)

No nothing in the error log refers to the sample database, but I do find errors for volvox which is strange considering it is working perfectly!?

Thanks again for the help Scott, I really appreciate it!

Regards,
Liam


On Thu, Aug 14, 2014 at 5:21 PM, Scott Cain <[hidden email]> wrote:
Hi Liam,

Please cc your responses to the GBrowse mailing list so other people can help and the resolution can be archived.

I don't see anything wrong with the GFF file itself (which isn't surprising since it's exactly the first gff file from the tutorial), though I wonder what it's really named: does it have a .gff or .gff3 appended to the end of the filename?  The underlying BioPerl code almost certainly requires that.

The only other thing I see that's not quite what I would expect is that the snippet of error log you sent references the volvox directory no the sample directory that you want to use.  When you try to load the sample database, does that cause anything to be written to the error log?

Scott



On Thu, Aug 14, 2014 at 12:03 PM, Liam O'Sullivan <[hidden email]> wrote:
Hello Scott,

Yup that is the exact error that I have, there is no issue with the pre-made datasets that were provided with installation. They work perfectly and can be modified.

Attached is my Gbrowse.conf file, the dataset conf file, the GFF3 and the end of the apache error file. 

I have simply made a copy of the volvox conf and GFF3 to ensure that it was not an error with my own conf/GFF3. The files are all located in the correct directories with the required permissions.

Thanks for the help Scott,
Regards,
Liam


On Mon, Aug 11, 2014 at 7:09 PM, Scott Cain <[hidden email]> wrote:
Hi Liam,

The most useful things for helping us help you debug this are the GBrowse.conf file, the dataset conf file, the top several lines of the GFF file and the last several lines of the apache error log.  The "not found" problem is pretty common, assuming you are referring to the case when you get a GBrowse page but you get in large read letters "Not found"; this is usually a GFF problem.  There are also file not found issues which are not uncommon and would be best be debugged with the combination of the config files and the apache error log (this usually happens when GBrowse is looking in one place for a file but you've put it somewhere else).

Scott



On Mon, Aug 11, 2014 at 12:28 PM, navillusol <[hidden email]> wrote:
Hello, I have been having issues with invoking anything but the tutorial
databases that come with gbrowse2. I have my own data that I wish to view
however after creating the necessary .conf files I still have no success.

So i decided to make an exact duplicate of the example volvox. I made a
seperate .conf file using the remarks gff3. I edited the main gbrowse.cof
file to allow access, I created a database in the correct path for this conf
file and placed the necessary folder in it. So everything is the exact same
and still it does not work. I get an error saying not found when trying to
invoke it.

the permissions on the databases are as follows:

drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 admin_uploads
*drwxrwxr-x 2 www-data www-data  4096 Aug 11 15:43 duplicate_volvox*
drwxrwxr-x 5 www-data www-data  4096 Jul 17 14:49 gbrowse_syn
drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 ideograms
drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 pop_demo
-rwxrwxr-x 1 www-data www-data 16384 Aug 11 17:02 users.sqlite
drwxrwxr-x 2 www-data www-data  4096 Aug 11 14:57 volvox
drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 yeast_chr1+2
drwxrwxr-x 2 www-data www-data  4096 Jul 17 15:21 yeast_scaffolds

I invoke the data using http://localhost/cgi-bin/gb2/gbrowse/volvoxDouble/
and the following is an image of the result (it is the same for all except
the tutorial files)

<http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712696/22.png>



I just do not understand what the problem is!? any help would be much
appreciated.






--
View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/Not-Found-tp5712696.html
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">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" target="_blank">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: Not Found

Matthew Johnson
Liam

So changing your gff file extension from .gff  to .gff3 did the trick? 

Thanks
Matt 

On Aug 15, 2014, at 8:32 AM, Scott Cain <[hidden email]> wrote:

Perhaps they are old errors for which you've already fixed the problem?  It's hard to say since your apache instance isn't configured to record the date and time at which the problem occurred.  As long as it's working now, I wouldn't worry too much about it.  Glad you got it sorted.

Scott



On Thu, Aug 14, 2014 at 12:37 PM, Liam O'Sullivan <[hidden email]> wrote:
Sorry for not cc-ing Scott, you were spot on that is exactly what the problem was (no .gff3 after the filename). I am so sorry what a trivial error to make. The sample database that I created is working perfectly now also! :-)

No nothing in the error log refers to the sample database, but I do find errors for volvox which is strange considering it is working perfectly!?

Thanks again for the help Scott, I really appreciate it!

Regards,
Liam


On Thu, Aug 14, 2014 at 5:21 PM, Scott Cain <[hidden email]> wrote:
Hi Liam,

Please cc your responses to the GBrowse mailing list so other people can help and the resolution can be archived.

I don't see anything wrong with the GFF file itself (which isn't surprising since it's exactly the first gff file from the tutorial), though I wonder what it's really named: does it have a .gff or .gff3 appended to the end of the filename?  The underlying BioPerl code almost certainly requires that.

The only other thing I see that's not quite what I would expect is that the snippet of error log you sent references the volvox directory no the sample directory that you want to use.  When you try to load the sample database, does that cause anything to be written to the error log?

Scott



On Thu, Aug 14, 2014 at 12:03 PM, Liam O'Sullivan <[hidden email]> wrote:
Hello Scott,

Yup that is the exact error that I have, there is no issue with the pre-made datasets that were provided with installation. They work perfectly and can be modified.

Attached is my Gbrowse.conf file, the dataset conf file, the GFF3 and the end of the apache error file. 

I have simply made a copy of the volvox conf and GFF3 to ensure that it was not an error with my own conf/GFF3. The files are all located in the correct directories with the required permissions.

Thanks for the help Scott,
Regards,
Liam


On Mon, Aug 11, 2014 at 7:09 PM, Scott Cain <[hidden email]> wrote:
Hi Liam,

The most useful things for helping us help you debug this are the GBrowse.conf file, the dataset conf file, the top several lines of the GFF file and the last several lines of the apache error log.  The "not found" problem is pretty common, assuming you are referring to the case when you get a GBrowse page but you get in large read letters "Not found"; this is usually a GFF problem.  There are also file not found issues which are not uncommon and would be best be debugged with the combination of the config files and the apache error log (this usually happens when GBrowse is looking in one place for a file but you've put it somewhere else).

Scott



On Mon, Aug 11, 2014 at 12:28 PM, navillusol <[hidden email]> wrote:
Hello, I have been having issues with invoking anything but the tutorial
databases that come with gbrowse2. I have my own data that I wish to view
however after creating the necessary .conf files I still have no success.

So i decided to make an exact duplicate of the example volvox. I made a
seperate .conf file using the remarks gff3. I edited the main gbrowse.cof
file to allow access, I created a database in the correct path for this conf
file and placed the necessary folder in it. So everything is the exact same
and still it does not work. I get an error saying not found when trying to
invoke it.

the permissions on the databases are as follows:

drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 admin_uploads
*drwxrwxr-x 2 www-data www-data  4096 Aug 11 15:43 duplicate_volvox*
drwxrwxr-x 5 www-data www-data  4096 Jul 17 14:49 gbrowse_syn
drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 ideograms
drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 pop_demo
-rwxrwxr-x 1 www-data www-data 16384 Aug 11 17:02 users.sqlite
drwxrwxr-x 2 www-data www-data  4096 Aug 11 14:57 volvox
drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 yeast_chr1+2
drwxrwxr-x 2 www-data www-data  4096 Jul 17 15:21 yeast_scaffolds

I invoke the data using http://localhost/cgi-bin/gb2/gbrowse/volvoxDouble/
and the following is an image of the result (it is the same for all except
the tutorial files)

<http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712696/22.png>



I just do not understand what the problem is!? any help would be much
appreciated.






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GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">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" target="_blank">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: Not Found

Scott Cain
Hi Matthew,

I don't think Liam had an extension at all.  Either gff or gff3 as extensions should work.

Scott



On Fri, Aug 15, 2014 at 12:30 PM, Matthew Johnson <[hidden email]> wrote:
Liam

So changing your gff file extension from .gff  to .gff3 did the trick? 

Thanks
Matt 

On Aug 15, 2014, at 8:32 AM, Scott Cain <[hidden email]> wrote:

Perhaps they are old errors for which you've already fixed the problem?  It's hard to say since your apache instance isn't configured to record the date and time at which the problem occurred.  As long as it's working now, I wouldn't worry too much about it.  Glad you got it sorted.

Scott



On Thu, Aug 14, 2014 at 12:37 PM, Liam O'Sullivan <[hidden email]> wrote:
Sorry for not cc-ing Scott, you were spot on that is exactly what the problem was (no .gff3 after the filename). I am so sorry what a trivial error to make. The sample database that I created is working perfectly now also! :-)

No nothing in the error log refers to the sample database, but I do find errors for volvox which is strange considering it is working perfectly!?

Thanks again for the help Scott, I really appreciate it!

Regards,
Liam


On Thu, Aug 14, 2014 at 5:21 PM, Scott Cain <[hidden email]> wrote:
Hi Liam,

Please cc your responses to the GBrowse mailing list so other people can help and the resolution can be archived.

I don't see anything wrong with the GFF file itself (which isn't surprising since it's exactly the first gff file from the tutorial), though I wonder what it's really named: does it have a .gff or .gff3 appended to the end of the filename?  The underlying BioPerl code almost certainly requires that.

The only other thing I see that's not quite what I would expect is that the snippet of error log you sent references the volvox directory no the sample directory that you want to use.  When you try to load the sample database, does that cause anything to be written to the error log?

Scott



On Thu, Aug 14, 2014 at 12:03 PM, Liam O'Sullivan <[hidden email]> wrote:
Hello Scott,

Yup that is the exact error that I have, there is no issue with the pre-made datasets that were provided with installation. They work perfectly and can be modified.

Attached is my Gbrowse.conf file, the dataset conf file, the GFF3 and the end of the apache error file. 

I have simply made a copy of the volvox conf and GFF3 to ensure that it was not an error with my own conf/GFF3. The files are all located in the correct directories with the required permissions.

Thanks for the help Scott,
Regards,
Liam


On Mon, Aug 11, 2014 at 7:09 PM, Scott Cain <[hidden email]> wrote:
Hi Liam,

The most useful things for helping us help you debug this are the GBrowse.conf file, the dataset conf file, the top several lines of the GFF file and the last several lines of the apache error log.  The "not found" problem is pretty common, assuming you are referring to the case when you get a GBrowse page but you get in large read letters "Not found"; this is usually a GFF problem.  There are also file not found issues which are not uncommon and would be best be debugged with the combination of the config files and the apache error log (this usually happens when GBrowse is looking in one place for a file but you've put it somewhere else).

Scott



On Mon, Aug 11, 2014 at 12:28 PM, navillusol <[hidden email]> wrote:
Hello, I have been having issues with invoking anything but the tutorial
databases that come with gbrowse2. I have my own data that I wish to view
however after creating the necessary .conf files I still have no success.

So i decided to make an exact duplicate of the example volvox. I made a
seperate .conf file using the remarks gff3. I edited the main gbrowse.cof
file to allow access, I created a database in the correct path for this conf
file and placed the necessary folder in it. So everything is the exact same
and still it does not work. I get an error saying not found when trying to
invoke it.

the permissions on the databases are as follows:

drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 admin_uploads
*drwxrwxr-x 2 www-data www-data  4096 Aug 11 15:43 duplicate_volvox*
drwxrwxr-x 5 www-data www-data  4096 Jul 17 14:49 gbrowse_syn
drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 ideograms
drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 pop_demo
-rwxrwxr-x 1 www-data www-data 16384 Aug 11 17:02 users.sqlite
drwxrwxr-x 2 www-data www-data  4096 Aug 11 14:57 volvox
drwxrwxr-x 2 www-data www-data  4096 Jul 17 14:49 yeast_chr1+2
drwxrwxr-x 2 www-data www-data  4096 Jul 17 15:21 yeast_scaffolds

I invoke the data using http://localhost/cgi-bin/gb2/gbrowse/volvoxDouble/
and the following is an image of the result (it is the same for all except
the tutorial files)

<http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712696/22.png>



I just do not understand what the problem is!? any help would be much
appreciated.






--
View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/Not-Found-tp5712696.html
Sent from the gmod-gbrowse mailing list archive at Nabble.com.

------------------------------------------------------------------------------
_______________________________________________
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">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" target="_blank">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" target="_blank">216-392-3087
Ontario Institute for Cancer Research
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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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