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Today's Topics:
1. Re: setting environment for sge scripts (Assaf Gordon)
2. Re: galaxy passing an incorrect directory to a script...
(Nate Coraor)
3. Suggestion on functionality for published workflows
(Timothy Hughes)
4. Re: Suggestion on functionality for published workflows
(Jelle Scholtalbers)
5. Getting sequences for multiple species from UCSC (Farhat Habib)
6. Re: Getting sequences for multiple species from UCSC
(Anton Nekrutenko)
7. Re: Collecting User Information on the Registration page
(Greg Von Kuster)
----------------------------------------------------------------------
Message: 1
Date: Tue, 20 Oct 2009 12:18:44 -0400
From: Assaf Gordon <gordon@cshl.edu>
To: Nate Coraor <nate@bx.psu.edu>
Cc: Andreas Kuntzagk <andreas.kuntzagk@mdc-berlin.de>,
galaxy-user@bx.psu.edu
Subject: Re: [galaxy-user] setting environment for sge scripts
Message-ID: <4ADDE2E4.3000209@cshl.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
SGE supports per-user defaults file called "~/.sge_request" ,
which can be used to set job's environment variables (and other qsub parameters).
I think it was mentioned in the galaxy-dev list (I don't remember by whom).
Example:
============
$ cat ~/.sge_request
-v PERL5LIB=/data/hannon/gordon/perl_modules/lib64/perl5
-v DUMMY=HELLO
============
Will add two environment variables (PERL5LIB and DUMMY) to each qsub job.
I guess this way you can also change the PATH.
see "man sge_request" or "man ge_request" (in some places it is mentioned as "ge_request" instead of "sge_request").
"man qsub" tells which options take precedence ( command-line VS script VS user-sge_request VS gloval-sge_request ).
Tested with SGE 6.1 and 6.2u3.
-gordon
Nate Coraor wrote, On 10/20/2009 11:51 AM:
> Andreas Kuntzagk wrote:
>
>> It is set in ~/.bashrc, which is source by ~/.bash_profile. If I
>> normally login to a cluster node via ssh it is set correctly. But if I
>> qsub a job, it is not read. Except when I set the "-V" switch. So I
>> either need to change gridengines behaviour or make galaxy use that switch.
>>
>> Is there a easy way to config how to submit cluster jobs?
>
> Andreas,
>
> SGE must not be running the shell as a login or interactive shell, which
> PBS does. You may want to check the 'INVOCATION' section of the bash(1)
> man page to see how you can force this.
>
> If you can't change how your shell is run by SGE, you could add what you
> need to the SGE job template in:
>
> galaxy_dist/lib/galaxy/jobs/runners/sge.py
>
> but this would be an ugly hack.
>
> --nate
> _______________________________________________
> galaxy-user mailing list
> galaxy-user@bx.psu.edu
> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
------------------------------
Message: 2
Date: Tue, 20 Oct 2009 13:05:53 -0400
From: Nate Coraor <nate@bx.psu.edu>
To: Nick Schurch <N.Schurch@dundee.ac.uk>
Cc: galaxy-user@bx.psu.edu
Subject: Re: [galaxy-user] galaxy passing an incorrect directory to a
script...
Message-ID: <4ADDEDF1.8010608@bx.psu.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Nick Schurch wrote:
> Does anyone have any idea why galaxy would pass a 'working directory'
> to the script rather than the directory where the files are actually
> stored? Is it that galaxy actually creates the files in the working
> directory and then moves them?
Hi Nick,
This was originally written for PBS file staging - since the
database/files/ directory was not mounted on cluster nodes, a path
common to the Galaxy application server and the node's tool execution
environment had to be used (the job working directory, which we put in NFS).
The current method to use this functionality is such:
If reading from an input's extra files, use $input.extra_files_path.
The extra_files_path attribute always points to the location in
database/files/.
If writing to an output's extra files, use $output.files_path. The
files_path attribute points to a directory in the job's working
directory. The framework will automatically relocate these extra files
to the real location in database/files/ as part of the job finish method.
This functionality was never well documented and is rather confusing, in
the future we plan to simplify it. A ticket exists for this:
http://bitbucket.org/galaxy/galaxy-central/issue/206/eliminate-the-use-of-files_path-in-tools
> I'm also really confused as to why the 'development' installation
> works fine, but the 'live' installation throws this error. Any insight
> would be greatly appreciated.
This shouldn't really be the case, it might help to see your tool's xml
and the code that generates the html, to understand how you're using the
extra files directory. Note that links to files in the extra files
directory should all be relative.
--nate
------------------------------
Message: 3
Date: Tue, 10 Nov 2009 23:36:50 +0100
From: Timothy Hughes <timothy.hughes@medisin.uio.no>
To: galaxy-user@bx.psu.edu
Subject: [galaxy-user] Suggestion on functionality for published
workflows
Message-ID:
<3508097b0911101436g39243390if960dae24a6b3df0@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
I have heard from jgoecks <http://bitbucket.org/jgoecks/> that the galaxy
team are working on a repository for all galaxy objects. I would like to
suggest that all workflows that are shared publically (published) have a
mandatory field that briefly describes their functionality and that the
repository have search functionality which enables a search of published
workflows using this field. I am sure their are loads of great workflows out
there which are either immediately usable or are easily adaptable. Getting
access to such workflows would also be an excellent way to learn Galaxy in a
complementary way to the screencasts.
While we are waiting for such functionality, perhaps Galaxy developers could
set up a simple page where the public histories / workflows can be posted.
The simplest solution might be just a check box on the sharing page ("post
link to publicly accessible page"), alternatively just a piece of text on
the sharing page encouraging users to manually post on specific forum or
mailing list.
Tim.
--
Tim Hughes PhD (http://digitised.info)
Medical Genetics Department
Oslo University Hospital Ullev?l
Kirkeveien 166
0407 Oslo
Norway
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Message: 4
Date: Wed, 11 Nov 2009 09:25:23 +0100
From: Jelle Scholtalbers <j.scholtalbers@gmail.com>
To: galaxy-user@bx.psu.edu
Subject: Re: [galaxy-user] Suggestion on functionality for published
workflows
Message-ID:
<b66932c30911110025t45b73d6amd777817dffe3d025@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
would it be an idea to post galaxy objects on myExperiment.org? It seems
like a good place to share these types of workflows and histories. Although
now mostly used by Taverna users, any kind of (scientific) digital object
can be placed there.
Cheers,
Jelle
2009/11/10 Timothy Hughes <timothy.hughes@medisin.uio.no>
> I have heard from jgoecks <http://bitbucket.org/jgoecks/> that the galaxy
> team are working on a repository for all galaxy objects. I would like to
> suggest that all workflows that are shared publically (published) have a
> mandatory field that briefly describes their functionality and that the
> repository have search functionality which enables a search of published
> workflows using this field. I am sure their are loads of great workflows out
> there which are either immediately usable or are easily adaptable. Getting
> access to such workflows would also be an excellent way to learn Galaxy in a
> complementary way to the screencasts.
>
> While we are waiting for such functionality, perhaps Galaxy developers
> could set up a simple page where the public histories / workflows can be
> posted. The simplest solution might be just a check box on the sharing page
> ("post link to publicly accessible page"), alternatively just a piece of
> text on the sharing page encouraging users to manually post on specific
> forum or mailing list.
>
> Tim.
>
> --
> Tim Hughes PhD (http://digitised.info)
> Medical Genetics Department
> Oslo University Hospital Ullev?l
> Kirkeveien 166
> 0407 Oslo
> Norway
>
>
>
> _______________________________________________
> galaxy-user mailing list
> galaxy-user@lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-user
>
>
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Message: 5
Date: Wed, 11 Nov 2009 20:08:10 +0530
From: Farhat Habib <farhat.habib@gmail.com>
To: galaxy-user@lists.bx.psu.edu
Subject: [galaxy-user] Getting sequences for multiple species from
UCSC
Message-ID:
<e7f0af090911110638u29b150ddp9089a19bdc9f7c48@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi all,
I am wondering if there is a way to download sequence information from
UCSC into Galaxy for multiple species. E.g, looking at a region of the
genome for Drosophila melanogaster, you can also see the level of
conservation across other insect species. Is it possible to get the
sequences from all species that align to that region of the genome in
Drosophila.
Thanks.
-Farhat
------------------------------
Message: 6
Date: Wed, 11 Nov 2009 10:02:29 -0500
From: Anton Nekrutenko <anton@bx.psu.edu>
To: Farhat Habib <farhat.habib@gmail.com>
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Getting sequences for multiple species from
UCSC
Message-ID: <CA80EFFC-D5C2-4786-9CF6-37CCF252B7CD@bx.psu.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
Farhat:
You can do this by extracting multiple species alignments for regions
of interest. Take a look at "Fetch Alignemnts" category of tools and
screencast 6 on this page:
http://galaxycast.org
Thanks,
anton
galaxy team
On Nov 11, 2009, at 9:38 AM, Farhat Habib wrote:
> Hi all,
>
> I am wondering if there is a way to download sequence information from
> UCSC into Galaxy for multiple species. E.g, looking at a region of the
> genome for Drosophila melanogaster, you can also see the level of
> conservation across other insect species. Is it possible to get the
> sequences from all species that align to that region of the genome in
> Drosophila.
>
> Thanks.
>
> -Farhat
> _______________________________________________
> galaxy-user mailing list
> galaxy-user@lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-user
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://galaxyproject.org
------------------------------
Message: 7
Date: Wed, 11 Nov 2009 13:15:16 -0500
From: Greg Von Kuster <greg@bx.psu.edu>
To: lentaing@jimmy.harvard.edu
Cc: galaxy-user@bx.psu.edu
Subject: Re: [galaxy-user] Collecting User Information on the
Registration page
Message-ID: <F6C72C49-740F-47E4-B402-0B5D5E72C338@bx.psu.edu>
Content-Type: text/plain; charset="us-ascii"; Format="flowed";
DelSp="yes"
Hello Len,
The ability to do this is now available in the Galaxy distribution -
for details, see our wiki at
http://bitbucket.org/galaxy/galaxy-central/wiki/Features/
UserInformation/UserInformation
New features like this will be added to the following wiki, and the
link to this Features wiki is included on our wiki home page.
http://bitbucket.org/galaxy/galaxy-central/wiki/Features/Features
On Aug 13, 2009, at 2:59 PM, lentaing@jimmy.harvard.edu wrote:
> Hi,
>
> We are interested in collecting more information about the user, e.g.
> which lab they're part of etc, as they register to use our local
> mirror of
> galaxy. Is there an easy way to add these fields to the registration
> page; is it also easy to store these values to the (galaxy) database?
>
> Thanks!
> Len
>
> _______________________________________________
> galaxy-user mailing list
> galaxy-user@bx.psu.edu
> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
>
>
Greg Von Kuster
Galaxy Development Team
greg@bx.psu.edu
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