I have never used myExperiment but it sounds like a good site to use for posting published workflows. The tricky bit is to get people to post their workflows there. Would Galaxy be willing to suggest that users publish workflows there? I think galaxy is great, but what it lacks at the moment is exactly something like this myExperiment.org which can provide the "social" elements: direct interaction between users, posting of workflows, collaboration, etc. I gather Galaxy is starting work in this direction, but perhaps it would be better to see to what extent galaxy could integrate with an existing solution. Tim. 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
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
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> 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
On Wed, Nov 11, 2009 at 7:15 PM, <galaxy-user-request@lists.bx.psu.edu>wrote:
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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)
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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
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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-fi...
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
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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