Queueing system and job parameters
Hi, I have a local Galaxy instance. I have tied the server to a local HPC and we use LSF for scheduling jobs. I was wondering how a user can submit a job from Galaxy while specifying a wall time and memory requirements for a job… Is this doable? Thanks, Prakash
Hi Prakash, You can use the relatively new job resource params feature to insert a standard set of params on any tool form. See the example at: https://bitbucket.org/galaxy/galaxy-central/src/tip/job_resource_params_conf... Here is an example of how we're using it on the Galaxy Test server: https://github.com/galaxyproject/usegalaxy-playbook/blob/master/files/galaxy... https://github.com/galaxyproject/usegalaxy-playbook/blob/master/files/galaxy... --nate On Wed, Sep 10, 2014 at 8:57 PM, Velayutham, Prakash (Prakash) < Prakash.Velayutham@cchmc.org> wrote:
Hi,
I have a local Galaxy instance. I have tied the server to a local HPC and we use LSF for scheduling jobs. I was wondering how a user can submit a job from Galaxy while specifying a wall time and memory requirements for a job… Is this doable?
Thanks, Prakash
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Hi Nate, Can you point me to the documentation that explains this in more detail? What version of Galaxy supports this? My build is at least 3 months old, probably even more. Thanks, Prakash On Sep 11, 2014, at 1:17 PM, Nate Coraor <nate@bx.psu.edu<mailto:nate@bx.psu.edu>> wrote: Hi Prakash, You can use the relatively new job resource params feature to insert a standard set of params on any tool form. See the example at: https://bitbucket.org/galaxy/galaxy-central/src/tip/job_resource_params_conf... Here is an example of how we're using it on the Galaxy Test server: https://github.com/galaxyproject/usegalaxy-playbook/blob/master/files/galaxy... https://github.com/galaxyproject/usegalaxy-playbook/blob/master/files/galaxy... --nate On Wed, Sep 10, 2014 at 8:57 PM, Velayutham, Prakash (Prakash) <Prakash.Velayutham@cchmc.org<mailto:Prakash.Velayutham@cchmc.org>> wrote: Hi, I have a local Galaxy instance. I have tied the server to a local HPC and we use LSF for scheduling jobs. I was wondering how a user can submit a job from Galaxy while specifying a wall time and memory requirements for a job… Is this doable? Thanks, Prakash ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Prakash, At this point, the documentation is the examples in job_resource_params_conf.xml.sample and job_conf.xml.sample. This code was in the August 2014 release, so you'll need to upgrade to use it. Here is the commit, which shows the changes to job_conf.xml.sample: https://bitbucket.org/galaxy/galaxy-central/commits/31b2924315d0b48fa7648ab4... --nate On Sun, Sep 14, 2014 at 8:34 AM, Velayutham, Prakash (Prakash) < Prakash.Velayutham@cchmc.org> wrote:
Hi Nate,
Can you point me to the documentation that explains this in more detail? What version of Galaxy supports this? My build is at least 3 months old, probably even more.
Thanks, Prakash
On Sep 11, 2014, at 1:17 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Hi Prakash,
You can use the relatively new job resource params feature to insert a standard set of params on any tool form. See the example at:
https://bitbucket.org/galaxy/galaxy-central/src/tip/job_resource_params_conf...
Here is an example of how we're using it on the Galaxy Test server:
https://github.com/galaxyproject/usegalaxy-playbook/blob/master/files/galaxy...
https://github.com/galaxyproject/usegalaxy-playbook/blob/master/files/galaxy...
--nate
On Wed, Sep 10, 2014 at 8:57 PM, Velayutham, Prakash (Prakash) < Prakash.Velayutham@cchmc.org> wrote:
Hi,
I have a local Galaxy instance. I have tied the server to a local HPC and we use LSF for scheduling jobs. I was wondering how a user can submit a job from Galaxy while specifying a wall time and memory requirements for a job… Is this doable?
Thanks, Prakash
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (2)
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Nate Coraor
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Velayutham, Prakash (Prakash)