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
Post by Sheldon McKayHi 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]
Post by Sheldon McKayGBrowse 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.
$ git clone https://github.com/GMOD/GBrowse.git
$ cd GBrowse
$ perl Build.PL
$ sudo ./Build install
Sheldon
On Mon, Sep 15, 2014 at 3:53 PM, Seth_m55 <[hidden email]
Post by Seth_m55Hi 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
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
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]
Post by Sheldon McKayHi 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]
Post by Seth MunhollandHello 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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