Missing Details panel in GBrowseSyn

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Missing Details panel in GBrowseSyn

Seth_m55
Hello Everyone,

I'm trying to configure GBrowseSyn on our webserver and figured I'd start small scale to learn my way around.  I isolated one scaffold from 2 different genomes and found where they align, converted it to a clustalw format then uploaded it to a mysql database using gbrowse_syn_load_alignments_msa as instructed in the tutorials.  I used the provided O.sativa synconf, conf, and gff3 files as a base and modified them to match my dataset.  I can open GBrowseSyn in a browser pointed at localhost, I can even highlight the areas that I know match, but no matter what I do the Details panel doesn't load.  All I get are Instructions, Search, Overview, and Display_Settings.  I've attached my synconf, conf, and gff3, and the clustalw files.  Any suggestions on where I should look to try and get the details Panel to appear?

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755

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OAC_Rex_PChr08.synconf (1K) Download Attachment
OAC_Rex_PChr08_synteny.conf (956 bytes) Download Attachment
P.acutifolius_synteny.conf (944 bytes) Download Attachment
OAC_Rex_PChr08.gff3 (1K) Download Attachment
P.acutifolius.gff3 (402 bytes) Download Attachment
corrected_Pseu_Pacu_Chr08_matches2.clw (6K) Download Attachment
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Re: Missing Details panel in GBrowseSyn

Sheldon McKay
Hi Seth,

Thanks for providing all of the information with your request.  One thing I notice is that your GFF reference sequence names are using a hyphen (Chr08_1-14305), while your alignment data uses an underscore (Chr08_1_14305).  Mis-matched refseq names break the linkage between the GFF and the alignment data.  If I recall correctly, gbrowse_syn will not display a details panel if there are no alignment data found.  I would recommend changing the GFF refseq names to also use the underscore.  I think a hyphen could potentially confuse the parser that extracts meta-data from the refseq ID in the alignment file.

If you are still stuck, could you send an excerpt of your apache error log?


Sheldon McKay


On Thu, Sep 11, 2014 at 4:25 PM, Seth Munholland <[hidden email]> wrote:
Hello Everyone,

I'm trying to configure GBrowseSyn on our webserver and figured I'd start small scale to learn my way around.  I isolated one scaffold from 2 different genomes and found where they align, converted it to a clustalw format then uploaded it to a mysql database using gbrowse_syn_load_alignments_msa as instructed in the tutorials.  I used the provided O.sativa synconf, conf, and gff3 files as a base and modified them to match my dataset.  I can open GBrowseSyn in a browser pointed at localhost, I can even highlight the areas that I know match, but no matter what I do the Details panel doesn't load.  All I get are Instructions, Search, Overview, and Display_Settings.  I've attached my synconf, conf, and gff3, and the clustalw files.  Any suggestions on where I should look to try and get the details Panel to appear?

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755

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Re: Missing Details panel in GBrowseSyn

Seth_m55
Hi Sheldon,

I went digging through some forums and found that I was running an old version of gbrowse.  I purged reisntalled and now I'm getting an apache error that an environment variable isn't set properly.  Another forum dive found this thread:
http://comments.gmane.org/gmane.science.biology.gmod.gbrowse/12492
where you say to do a fresh git pull to fix things.  I did a git clone of the GBrowse repository as outlined here:
http://gmod.org/wiki/GBrowse_syn_Tutorial_2013#Installing_GBrowse_syn
But that didn't get it to load, Unfortunately, I installed the latest version via CPAN and I'm new to git commands.  What is the repository I need to point git pull at to update the environment variable correctly?


Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755

On Sun, Sep 14, 2014 at 10:56 AM, Sheldon McKay [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Seth,

Thanks for providing all of the information with your request.  One thing I notice is that your GFF reference sequence names are using a hyphen (Chr08_1-14305), while your alignment data uses an underscore (Chr08_1_14305).  Mis-matched refseq names break the linkage between the GFF and the alignment data.  If I recall correctly, gbrowse_syn will not display a details panel if there are no alignment data found.  I would recommend changing the GFF refseq names to also use the underscore.  I think a hyphen could potentially confuse the parser that extracts meta-data from the refseq ID in the alignment file.

If you are still stuck, could you send an excerpt of your apache error log?


Sheldon McKay


On Thu, Sep 11, 2014 at 4:25 PM, Seth Munholland <[hidden email]> wrote:
Hello Everyone,

I'm trying to configure GBrowseSyn on our webserver and figured I'd start small scale to learn my way around.  I isolated one scaffold from 2 different genomes and found where they align, converted it to a clustalw format then uploaded it to a mysql database using gbrowse_syn_load_alignments_msa as instructed in the tutorials.  I used the provided O.sativa synconf, conf, and gff3 files as a base and modified them to match my dataset.  I can open GBrowseSyn in a browser pointed at localhost, I can even highlight the areas that I know match, but no matter what I do the Details panel doesn't load.  All I get are Instructions, Search, Overview, and Display_Settings.  I've attached my synconf, conf, and gff3, and the clustalw files.  Any suggestions on where I should look to try and get the details Panel to appear?

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755

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Re: Missing Details panel in GBrowseSyn

Sheldon McKay
GBrowse on CPAN does not have the latest patches.  You will want to get GBrowse and re-install.  
Things may get messy if you mix CPAN and the git version, so I would purge (except your data) before the update.

$ cd GBrowse
$ perl Build.PL
$ sudo ./Build install 

Sheldon


On Mon, Sep 15, 2014 at 3:53 PM, Seth_m55 <[hidden email]> wrote:
Hi Sheldon,

I went digging through some forums and found that I was running an old version of gbrowse.  I purged reisntalled and now I'm getting an apache error that an environment variable isn't set properly.  Another forum dive found this thread:
http://comments.gmane.org/gmane.science.biology.gmod.gbrowse/12492
where you say to do a fresh git pull to fix things.  I did a git clone of the GBrowse repository as outlined here:
http://gmod.org/wiki/GBrowse_syn_Tutorial_2013#Installing_GBrowse_syn
But that didn't get it to load, Unfortunately, I installed the latest version via CPAN and I'm new to git commands.  What is the repository I need to point git pull at to update the environment variable correctly?


Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755

On Sun, Sep 14, 2014 at 10:56 AM, Sheldon McKay [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Seth,

Thanks for providing all of the information with your request.  One thing I notice is that your GFF reference sequence names are using a hyphen (Chr08_1-14305), while your alignment data uses an underscore (Chr08_1_14305).  Mis-matched refseq names break the linkage between the GFF and the alignment data.  If I recall correctly, gbrowse_syn will not display a details panel if there are no alignment data found.  I would recommend changing the GFF refseq names to also use the underscore.  I think a hyphen could potentially confuse the parser that extracts meta-data from the refseq ID in the alignment file.

If you are still stuck, could you send an excerpt of your apache error log?


Sheldon McKay


On Thu, Sep 11, 2014 at 4:25 PM, Seth Munholland <[hidden email]> wrote:
Hello Everyone,

I'm trying to configure GBrowseSyn on our webserver and figured I'd start small scale to learn my way around.  I isolated one scaffold from 2 different genomes and found where they align, converted it to a clustalw format then uploaded it to a mysql database using gbrowse_syn_load_alignments_msa as instructed in the tutorials.  I used the provided O.sativa synconf, conf, and gff3 files as a base and modified them to match my dataset.  I can open GBrowseSyn in a browser pointed at localhost, I can even highlight the areas that I know match, but no matter what I do the Details panel doesn't load.  All I get are Instructions, Search, Overview, and Display_Settings.  I've attached my synconf, conf, and gff3, and the clustalw files.  Any suggestions on where I should look to try and get the details Panel to appear?

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755

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View this message in context: Re: Missing Details panel in GBrowseSyn
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Re: Missing Details panel in GBrowseSyn

Scott Cain
Hi Seth,

In addition to Sheldon's comments (doing an install from the git clone), I'd point out that the environment variable it's talking about is probably being set in an apache configuration file called (I think) gbrowse.conf and it is wherever your version of apache like to put those things (for example, Ubuntu likes to put it in /etc/apache2/conf.d/). When GBrowse is installed correctly, it should set that variable for you, but when you have multiple installations (like you tried several different ways to install GBrowse), apache can be looking at the wrong conf file.

Scott


On Mon, Sep 15, 2014 at 5:49 PM, Sheldon McKay <[hidden email]> wrote:
GBrowse on CPAN does not have the latest patches.  You will want to get GBrowse and re-install.  
Things may get messy if you mix CPAN and the git version, so I would purge (except your data) before the update.

$ cd GBrowse
$ perl Build.PL
$ sudo ./Build install 

Sheldon


On Mon, Sep 15, 2014 at 3:53 PM, Seth_m55 <[hidden email]> wrote:
Hi Sheldon,

I went digging through some forums and found that I was running an old version of gbrowse.  I purged reisntalled and now I'm getting an apache error that an environment variable isn't set properly.  Another forum dive found this thread:
http://comments.gmane.org/gmane.science.biology.gmod.gbrowse/12492
where you say to do a fresh git pull to fix things.  I did a git clone of the GBrowse repository as outlined here:
http://gmod.org/wiki/GBrowse_syn_Tutorial_2013#Installing_GBrowse_syn
But that didn't get it to load, Unfortunately, I installed the latest version via CPAN and I'm new to git commands.  What is the repository I need to point git pull at to update the environment variable correctly?


Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755

On Sun, Sep 14, 2014 at 10:56 AM, Sheldon McKay [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Seth,

Thanks for providing all of the information with your request.  One thing I notice is that your GFF reference sequence names are using a hyphen (Chr08_1-14305), while your alignment data uses an underscore (Chr08_1_14305).  Mis-matched refseq names break the linkage between the GFF and the alignment data.  If I recall correctly, gbrowse_syn will not display a details panel if there are no alignment data found.  I would recommend changing the GFF refseq names to also use the underscore.  I think a hyphen could potentially confuse the parser that extracts meta-data from the refseq ID in the alignment file.

If you are still stuck, could you send an excerpt of your apache error log?


Sheldon McKay


On Thu, Sep 11, 2014 at 4:25 PM, Seth Munholland <[hidden email]> wrote:
Hello Everyone,

I'm trying to configure GBrowseSyn on our webserver and figured I'd start small scale to learn my way around.  I isolated one scaffold from 2 different genomes and found where they align, converted it to a clustalw format then uploaded it to a mysql database using gbrowse_syn_load_alignments_msa as instructed in the tutorials.  I used the provided O.sativa synconf, conf, and gff3 files as a base and modified them to match my dataset.  I can open GBrowseSyn in a browser pointed at localhost, I can even highlight the areas that I know match, but no matter what I do the Details panel doesn't load.  All I get are Instructions, Search, Overview, and Display_Settings.  I've attached my synconf, conf, and gff3, and the clustalw files.  Any suggestions on where I should look to try and get the details Panel to appear?

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755

------------------------------------------------------------------------------
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When you want reliability, choose Perforce
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View this message in context: Re: Missing Details panel in GBrowseSyn
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--
------------------------------------------------------------------------
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: Missing Details panel in GBrowseSyn

Seth_m55
Hi guys,

I purged the CPAN gbrowse and installed from a fresh git pull.  I got it all configured and rebuilt the demo Oryza data to make sure it was working and it all shows up now.  These are the apache error.log entries for pointing at the Oryza DB, showing the rice example, showing the wild_rice example, pointing at my test DB, showing my OAC_Rex example, and showing my Pacutifolius example.  I waited for a minute or two between each action to make sure the error log entries could be clearly associated with each action.

[Tue Sep 16 10:49:54 2014] [error] [client 192.168.0.1] [Tue Sep 16 10:49:54 2014] gbrowse_syn: Use of uninitialized value $_[1] in hash element at /usr/local/share/perl/5.14.2/Bio/Graphics/FeatureFile.pm line 1143., referer: http://www.bioinfo.uwindsor.ca/cgi-bin/gb2/gbrowse_syn/OAC_Rex_PChr08/?search_src=OAC_Rex_PChr08;name=Chr08_1-14305:4948..5676
[Tue Sep 16 10:53:02 2014] [error] [client 192.168.0.1] [Tue Sep 16 10:53:02 2014] gbrowse_syn: Use of uninitialized value $rest[1] in join or string at (eval 119) line 15., referer: http://www.bioinfo.uwindsor.ca/cgi-bin/gb2/gbrowse_syn/oryza/
[Tue Sep 16 10:58:09 2014] [error] [client 192.168.0.1] [Tue Sep 16 10:58:09 2014] gbrowse_syn: Use of uninitialized value $rest[1] in join or string at (eval 119) line 15., referer: http://www.bioinfo.uwindsor.ca/cgi-bin/gb2/gbrowse_syn/oryza/?search_src=rice;name=3:337601..383524
[Tue Sep 16 11:00:09 2014] [error] [client 192.168.0.1] [Tue Sep 16 11:00:09 2014] gbrowse_syn: Use of uninitialized value $_[1] in hash element at /usr/local/share/perl/5.14.2/Bio/Graphics/FeatureFile.pm line 1143., referer: http://www.bioinfo.uwindsor.ca/cgi-bin/gb2/gbrowse_syn/oryza/?search_src=wild_rice;name=3:1..400000
[Tue Sep 16 11:01:25 2014] [error] [client 192.168.0.1] [Tue Sep 16 11:01:25 2014] gbrowse_syn: Use of uninitialized value $rest[1] in join or string at (eval 119) line 15., referer: http://www.bioinfo.uwindsor.ca/cgi-bin/gb2/gbrowse_syn/OAC_Rex_PChr08/
[Tue Sep 16 11:05:00 2014] [error] [client 192.168.0.1] [Tue Sep 16 11:05:00 2014] gbrowse_syn: Use of uninitialized value $rest[1] in join or string at (eval 119) line 15., referer: http://www.bioinfo.uwindsor.ca/cgi-bin/gb2/gbrowse_syn/OAC_Rex_PChr08/?search_src=OAC_Rex_PChr08;name=Chr08_1-14305:4948..5676

I am back where I was, with no details track showing up, but everything else seems to be running.  Now I think the issue is that GBrowseSyn can't find the data in the mysql DB to present it as Sheldon first suggested.

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755

On Mon, Sep 15, 2014 at 7:23 PM, Scott Cain [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Seth,

In addition to Sheldon's comments (doing an install from the git clone), I'd point out that the environment variable it's talking about is probably being set in an apache configuration file called (I think) gbrowse.conf and it is wherever your version of apache like to put those things (for example, Ubuntu likes to put it in /etc/apache2/conf.d/). When GBrowse is installed correctly, it should set that variable for you, but when you have multiple installations (like you tried several different ways to install GBrowse), apache can be looking at the wrong conf file.

Scott


On Mon, Sep 15, 2014 at 5:49 PM, Sheldon McKay <[hidden email]> wrote:
GBrowse on CPAN does not have the latest patches.  You will want to get GBrowse and re-install.  
Things may get messy if you mix CPAN and the git version, so I would purge (except your data) before the update.

$ cd GBrowse
$ perl Build.PL
$ sudo ./Build install 

Sheldon


On Mon, Sep 15, 2014 at 3:53 PM, Seth_m55 <[hidden email]> wrote:
Hi Sheldon,

I went digging through some forums and found that I was running an old version of gbrowse.  I purged reisntalled and now I'm getting an apache error that an environment variable isn't set properly.  Another forum dive found this thread:
http://comments.gmane.org/gmane.science.biology.gmod.gbrowse/12492
where you say to do a fresh git pull to fix things.  I did a git clone of the GBrowse repository as outlined here:
http://gmod.org/wiki/GBrowse_syn_Tutorial_2013#Installing_GBrowse_syn
But that didn't get it to load, Unfortunately, I installed the latest version via CPAN and I'm new to git commands.  What is the repository I need to point git pull at to update the environment variable correctly?


Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755

On Sun, Sep 14, 2014 at 10:56 AM, Sheldon McKay [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Seth,

Thanks for providing all of the information with your request.  One thing I notice is that your GFF reference sequence names are using a hyphen (Chr08_1-14305), while your alignment data uses an underscore (Chr08_1_14305).  Mis-matched refseq names break the linkage between the GFF and the alignment data.  If I recall correctly, gbrowse_syn will not display a details panel if there are no alignment data found.  I would recommend changing the GFF refseq names to also use the underscore.  I think a hyphen could potentially confuse the parser that extracts meta-data from the refseq ID in the alignment file.

If you are still stuck, could you send an excerpt of your apache error log?


Sheldon McKay


On Thu, Sep 11, 2014 at 4:25 PM, Seth Munholland <[hidden email]> wrote:
Hello Everyone,

I'm trying to configure GBrowseSyn on our webserver and figured I'd start small scale to learn my way around.  I isolated one scaffold from 2 different genomes and found where they align, converted it to a clustalw format then uploaded it to a mysql database using gbrowse_syn_load_alignments_msa as instructed in the tutorials.  I used the provided O.sativa synconf, conf, and gff3 files as a base and modified them to match my dataset.  I can open GBrowseSyn in a browser pointed at localhost, I can even highlight the areas that I know match, but no matter what I do the Details panel doesn't load.  All I get are Instructions, Search, Overview, and Display_Settings.  I've attached my synconf, conf, and gff3, and the clustalw files.  Any suggestions on where I should look to try and get the details Panel to appear?

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755

------------------------------------------------------------------------------
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Re: Missing Details panel in GBrowseSyn

Seth_m55
In reply to this post by Scott Cain
Hi guys,

I figured out my mistake.  I was labeling the organism OAC_Rex in the clustalw file, but pointing at it as OAC_Rex_PChr08 in the conf files.  It is now showing up jsut fine, and with the single version setup I notice our GBrowse is actually running much smoother than it was before.  Thanks for all your help!

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755

On Tue, Sep 16, 2014 at 11:47 AM, Seth Munholland <[hidden email]> wrote:
Hi guys,

I purged the CPAN gbrowse and installed from a fresh git pull.  I got it all configured and rebuilt the demo Oryza data to make sure it was working and it all shows up now.  These are the apache error.log entries for pointing at the Oryza DB, showing the rice example, showing the wild_rice example, pointing at my test DB, showing my OAC_Rex example, and showing my Pacutifolius example.  I waited for a minute or two between each action to make sure the error log entries could be clearly associated with each action.

[Tue Sep 16 10:49:54 2014] [error] [client 192.168.0.1] [Tue Sep 16 10:49:54 2014] gbrowse_syn: Use of uninitialized value $_[1] in hash element at /usr/local/share/perl/5.14.2/Bio/Graphics/FeatureFile.pm line 1143., referer: http://www.bioinfo.uwindsor.ca/cgi-bin/gb2/gbrowse_syn/OAC_Rex_PChr08/?search_src=OAC_Rex_PChr08;name=Chr08_1-14305:4948..5676
[Tue Sep 16 10:53:02 2014] [error] [client 192.168.0.1] [Tue Sep 16 10:53:02 2014] gbrowse_syn: Use of uninitialized value $rest[1] in join or string at (eval 119) line 15., referer: http://www.bioinfo.uwindsor.ca/cgi-bin/gb2/gbrowse_syn/oryza/
[Tue Sep 16 10:58:09 2014] [error] [client 192.168.0.1] [Tue Sep 16 10:58:09 2014] gbrowse_syn: Use of uninitialized value $rest[1] in join or string at (eval 119) line 15., referer: http://www.bioinfo.uwindsor.ca/cgi-bin/gb2/gbrowse_syn/oryza/?search_src=rice;name=3:337601..383524
[Tue Sep 16 11:00:09 2014] [error] [client 192.168.0.1] [Tue Sep 16 11:00:09 2014] gbrowse_syn: Use of uninitialized value $_[1] in hash element at /usr/local/share/perl/5.14.2/Bio/Graphics/FeatureFile.pm line 1143., referer: http://www.bioinfo.uwindsor.ca/cgi-bin/gb2/gbrowse_syn/oryza/?search_src=wild_rice;name=3:1..400000
[Tue Sep 16 11:01:25 2014] [error] [client 192.168.0.1] [Tue Sep 16 11:01:25 2014] gbrowse_syn: Use of uninitialized value $rest[1] in join or string at (eval 119) line 15., referer: http://www.bioinfo.uwindsor.ca/cgi-bin/gb2/gbrowse_syn/OAC_Rex_PChr08/
[Tue Sep 16 11:05:00 2014] [error] [client 192.168.0.1] [Tue Sep 16 11:05:00 2014] gbrowse_syn: Use of uninitialized value $rest[1] in join or string at (eval 119) line 15., referer: http://www.bioinfo.uwindsor.ca/cgi-bin/gb2/gbrowse_syn/OAC_Rex_PChr08/?search_src=OAC_Rex_PChr08;name=Chr08_1-14305:4948..5676

I am back where I was, with no details track showing up, but everything else seems to be running.  Now I think the issue is that GBrowseSyn can't find the data in the mysql DB to present it as Sheldon first suggested.

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755

On Mon, Sep 15, 2014 at 7:23 PM, Scott Cain [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Seth,

In addition to Sheldon's comments (doing an install from the git clone), I'd point out that the environment variable it's talking about is probably being set in an apache configuration file called (I think) gbrowse.conf and it is wherever your version of apache like to put those things (for example, Ubuntu likes to put it in /etc/apache2/conf.d/). When GBrowse is installed correctly, it should set that variable for you, but when you have multiple installations (like you tried several different ways to install GBrowse), apache can be looking at the wrong conf file.

Scott


On Mon, Sep 15, 2014 at 5:49 PM, Sheldon McKay <[hidden email]> wrote:
GBrowse on CPAN does not have the latest patches.  You will want to get GBrowse and re-install.  
Things may get messy if you mix CPAN and the git version, so I would purge (except your data) before the update.

$ cd GBrowse
$ perl Build.PL
$ sudo ./Build install 

Sheldon


On Mon, Sep 15, 2014 at 3:53 PM, Seth_m55 <[hidden email]> wrote:
Hi Sheldon,

I went digging through some forums and found that I was running an old version of gbrowse.  I purged reisntalled and now I'm getting an apache error that an environment variable isn't set properly.  Another forum dive found this thread:
http://comments.gmane.org/gmane.science.biology.gmod.gbrowse/12492
where you say to do a fresh git pull to fix things.  I did a git clone of the GBrowse repository as outlined here:
http://gmod.org/wiki/GBrowse_syn_Tutorial_2013#Installing_GBrowse_syn
But that didn't get it to load, Unfortunately, I installed the latest version via CPAN and I'm new to git commands.  What is the repository I need to point git pull at to update the environment variable correctly?


Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755

On Sun, Sep 14, 2014 at 10:56 AM, Sheldon McKay [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Seth,

Thanks for providing all of the information with your request.  One thing I notice is that your GFF reference sequence names are using a hyphen (Chr08_1-14305), while your alignment data uses an underscore (Chr08_1_14305).  Mis-matched refseq names break the linkage between the GFF and the alignment data.  If I recall correctly, gbrowse_syn will not display a details panel if there are no alignment data found.  I would recommend changing the GFF refseq names to also use the underscore.  I think a hyphen could potentially confuse the parser that extracts meta-data from the refseq ID in the alignment file.

If you are still stuck, could you send an excerpt of your apache error log?


Sheldon McKay


On Thu, Sep 11, 2014 at 4:25 PM, Seth Munholland <[hidden email]> wrote:
Hello Everyone,

I'm trying to configure GBrowseSyn on our webserver and figured I'd start small scale to learn my way around.  I isolated one scaffold from 2 different genomes and found where they align, converted it to a clustalw format then uploaded it to a mysql database using gbrowse_syn_load_alignments_msa as instructed in the tutorials.  I used the provided O.sativa synconf, conf, and gff3 files as a base and modified them to match my dataset.  I can open GBrowseSyn in a browser pointed at localhost, I can even highlight the areas that I know match, but no matter what I do the Details panel doesn't load.  All I get are Instructions, Search, Overview, and Display_Settings.  I've attached my synconf, conf, and gff3, and the clustalw files.  Any suggestions on where I should look to try and get the details Panel to appear?

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755

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GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
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