Gmod-gbrowse -- Info, bug reports, developers for the Generic Genome Browser

Wes Barris | 1 Oct 2009 02:35

Re: Running gbrowse 1.7 and gbrowse2 concurrently?

Lincoln Stein wrote:
> Hi All,
> 
> I've just done a big rename of GBrowse to GBrowse2 in all the library 
> files that GBrowse2 uses. Some of the plugins may be broken, but basic 
> functionality checks out. If you are adventurous you can grab it from 
> SVN. Otherwise I will be releasing a new version in a couple of days 
> that includes these changes and other bug fixes.
> 
> In theory, at least, you'll be able to do a "make install" on 1.7, a 
> "build install" on 2.0, and have them both work side-by-side.

This is still not working for me.  I did an svn checkout:

wes <at> bioweb> svn co https://gmod.svn.sourceforge.net/svnroot/gmod/Generic-Genome-Browser/trunk Generic-Genome-Browser
Checked out revision 22129.

After running ./Build install on the new gbrowse2 version, the old,
previously installed 1.7 version breaks with these errors reported
by apache:

[Thu Oct 01 10:28:59 2009] [error] [client 140.253.153.217] Undefined subroutine &main::conf_dir
called at /htdocs/gbrowse/gbrowse.cgi line 130.
[Thu Oct 01 10:28:59 2009] [error] [client 140.253.153.217] Premature end of script headers: gbrowse.cgi

Since I've been trying to do this before you made the changes,
is there something that I should manually remove from my /usr/bin/perl5
tree?

> Lincoln

(Continue reading)

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陈冠华 | 1 Oct 2009 16:44

error when loading data

Hi all,

I met an error when loading the data by the script. Is that related to mysql file's access permission.Since it used to work well but not after the linux system do security upgrade.
Thanks.

>perl bp_seqfeature_load.pl -f -d testproject -u root -p 1 /home/cghhust/data/recomb.gff

DBD::mysql::st execute failed: Table 'meta' is read only at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1239.

-------------------- EXCEPTION --------------------
MSG: Table 'meta' is read only

--
Guanhua(Josh) Chen

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Scott Cain | 1 Oct 2009 17:53

Re: error when loading data

Hi Josh,

Apparently you have to re-grant permission to do things with the  
tables in your database.  Try:

   mysql -u root -e 'grant all privileges on testproject.* to  
root <at> localhost'
   mysql -u root -e 'grant file on *.* to root <at> localhost'

Scott

On Oct 1, 2009, at 10:44 AM, 陈冠华 wrote:

> Hi all,
>
> I met an error when loading the data by the script. Is that related  
> to mysql file's access permission.Since it used to work well but not  
> after the linux system do security upgrade.
> Thanks.
>
> >perl bp_seqfeature_load.pl -f -d testproject -u root -p 1 /home/ 
> cghhust/data/recomb.gff
>
> DBD::mysql::st execute failed: Table 'meta' is read only at /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1239.
>
> -------------------- EXCEPTION --------------------
> MSG: Table 'meta' is read only
>
> -- 
> Guanhua(Josh) Chen
> ------------------------------------------------------------------------------
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Ontario Institute for Cancer Research

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James Ward | 1 Oct 2009 22:29

[SOLVED] libgd segfaults with GBrowse2 and multiple search results

I just wanted to post a solution, or potential solution, for any others who may be experiencing the mysterious libgd.so segfault errors. In my case the errors happened whenever a search result returned multiple regions. The page returned would be empty below the "Search" section, abruptly ending before rendering the Overview and any other sections on the web page.

I'm running Ubuntu, and I saw the error in /var/log/kern.log:

gbrowse[10265]: segfault at 7ffff7a63ff8 ip 00007f70eaf9a355 sp 00007ffff7a64000 error 6 in libgd.so.2.0.0[7f70eaf90000+22000]

I tried a ton of stuff, compiled numerous libgd's, uninstalled/reinstalled about every library, package, Perl module, noticed the poor PHP people and their GD imagerotate() problems, etc etc! Ultimately, as I should've guessed, I had a duplicate Perl module in my filesystem which was causing conflict, in part because the older Perl module occurred first in the <at> INC.

Bio/Graphics/Glyph/ideogram.pm

If you have more than one... :-) yeah, you don't want more than one, delete the older one. Good news, BOOYAH the search works great now!

I should mention that there were other duplicate/older Perl modules -- obviously the remnants of GBrowse 1.x. I'd suggest to others, if you have GBrowse2 problems, look for any duplicate modules to see if you've got the old residue of GBrowse 1.x in your filesystem.

Hope this solution helps someone else enjoy GBrowse2!

Best regards,

James M. Ward
Bioinformatics and Computational Biology
Duke University Neurobiology
jmw86069 <at> gmail.com
james.m.ward-4+jYJfmkT58@public.gmane.org

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Liisa Koski | 2 Oct 2009 04:19

Liisa Koski is out of the office.


I will be out of the office starting  2009-10-01 and will not return until
2009-10-02.

In case of an urgent request please email support@...

Thank you,
Liisa

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Lincoln Stein | 2 Oct 2009 16:06

Re: INSERT command denied on Reset, GBrowse 2

Hi Neil,

It turns out that there was a bug in DBI/mysql.pm that causes the backend to try to insert a sequence ID whenever it searches for a sequence that is unknown. My guess is that you have your initial feature set to an invalid sequence id, so that when you reset, it searches for that sequence id and fails.

The enclosed diff fixes the bug in the mysql adaptor, which is part of BioPerl. It is also in bioperl-live SVN, but unfortunately did not make it into the recent bioperl release.

Lincoln

On Fri, Sep 11, 2009 at 1:45 AM, Neil Saunders <neilfws-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:

Just noticed something new on a GBrowse 2 installation (CVS, SVN
Bioperl, Ubuntu 9.04, Apache 2.2.11, MySQL 5.0.75).

Clicking the 'reset' link gives an incompletely rendered initial display
and this error in the Apache log:

INSERT command denied to user 'genome' <at> 'localhost' for table
'locationlist' at
/usr/local/share/perl/5.10.0/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1466.

My impression was that the MySQL user needs only SELECT privilege. Why
is this INSERT appearing?

thanks
Neil Saunders
--
Statistical Bioinformatics - Health
CSIRO Mathematical and Information Sciences
Locked Bag 17, North Ryde, NSW 1670, Australia

http://friendfeed.com/neilfws

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Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q@public.gmane.org>

Attachment (insert_bug.diff): text/x-diff, 939 bytes

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Shane Brubaker | 3 Oct 2009 01:32

Question about sequence and blast interface

Hi, I have a couple of general questions about setting up a GBrowse site for the first time. I am setting up a site for a genome which contains several hundred scaffolds. One thing we would like to do is be able to BLAST a gene and then have a link to the appropriate location on the correct scaffold, and then go into GBrowse from there.

1. Is there a package out there that makes a BLAST web interface that then links into GBrowse? I have seen quite a few places that have set this up themselves, but I’m wondering if there is something out there pre-packaged that would help me do this? Keyword searching on gene annotations is another method of getting in that is desired.

2. Can you load the nucleotide sequence of the entire scaffold into GBrowse (I am using Chado as the back-end by the way) such that people could then select/highlight a region on the scaffold and then copy the sequence to their clipboard?

3. In general what are good ways to handle implementations where you have a lot of scaffolds?

Thanks very much for your help,

Shane Brubaker

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Neil.Saunders | 3 Oct 2009 03:20

Re: INSERT command denied on Reset, GBrowse 2

> The enclosed diff fixes the bug in the mysql adaptor, which is part of BioPerl.
> It is also in bioperl-live SVN, but unfortunately did not make it into the recent bioperl release.

That's great, thanks.  Will try that out in a couple of weeks (after vacation).

Neil
--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...<mailto:Renata.Musa@...>>

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Yuri Bendana | 3 Oct 2009 03:40

tracking Gbrowse2 releases

I recently upgraded to the Gbrowse tagged 'release-1_997' and it's been working great. But it doesn't appear that these releases are announced on this list. Can you announce the tagged releases of Gbrowse2?

thanks,

yuri

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Peter Ruzanov | 5 Oct 2009 04:12

GBrowse language support issue

I'm not sure that is the right place to send this,
but I recently found that at least russian support for GBrowse may be broken - see the attached screenshot. I've tried different Encoding settings - Auto-detect on-off, etc. but the problem persists. (I used Firefox 3.0.14 Windows XP). You may see in the attached image that some symbols get substituted with black diamonds with '?' inside.
regards,

Peter

Peter Ruzanov, PhD

Scientific Associate
Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3
(416) 673-8579

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