Re: [galaxy-dev] How to configure galaxy with a cluster

20 Jul 2014

      Hi Ben,

sorry but we do not run a Torque setup.

Do you have any concrete questions or error messages?

Cheers,
Bjoern

Am 17.07.2014 04:10, schrieb 王渭巍:
...
Hi, Bjoern
         Would you share your  procedure to make some tools to run on a cluster.
         I have tried https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster using Torque, but got errors.
         I think maybe it's job_conf.xml. Would you share yours?  Thanks a lot
Ben
From: Björn Grüning
Date: 2014-07-16 16:34
To: 王渭巍; Thomas Bellembois; galaxy-dev
Subject: Re: [galaxy-dev] How to configure galaxy with a cluster
Hi Ben,
that is not possible at the moment. The idea is to keep the
user-inferface as easy as possible for the user. You, as admin, can
decide which resource a specific tool with a specific input will use.
You will never see any options like that in a tool, but you can write a
tool by yourself if you like, or "enhance" the megablast tool.
Cheers,
Bjoern
Am 16.07.2014 09:43, schrieb 王渭巍:
...
Thanks a lot, Thomas! It really helps, I added tools section followed your suggestion...
here is my job_conf.xml ( I am using Torque,  I have 3 servers. One for galaxy server, two for cluster computing.  )
<?xml version="1.0"?>
<job_conf>
<plugins>
<plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner"/>
</plugins>
<destinations default="pbs_default">
<destination id="pbs_default" runner="pbs"/>
</destination>
<destination id="long_jobs" runner="pbs">
<param id="Resource_List">walltime=72:00:00,nodes=1:ppn=8</param>
<param id="-p">128</param>
</destination>
</destinations>
<tools>
<tool id="megablast_wrapper" destination="long_jobs"/>
</tools>
</job_conf>
and still no cluster options in "megablast" item.  How can I see cluster options in the page, for example, the page will let me choose to use local server or a cluster.
Ben
From: Thomas Bellembois
Date: 2014-07-15 17:41
To: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] How to configure galaxy with a cluster
Hello Ben,
you can configure your Galaxy instance to use your cluster in the
job_conf.xml file:
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
You can set up your instance to use your cluster by default for all jobs
or only for specific jobs.
Here is a part of my job_conf.xml for example:
<plugins>
<!-- LOCAL JOBS -->
          <plugin id="local" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
<!-- SUN GRID ENGINE -->
          <plugin id="sge" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
      </plugins>
<handlers default="handlers">
          <handler id="handler0" tags="handlers"/>
          <handler id="handler1" tags="handlers"/>
      </handlers>
<destinations default="sge_default">
          <destination id="local" runner="local"/>
          <destination id="sge_default" runner="sge">
            <param id="nativeSpecification">-r yes -b n -cwd -S /bin/bash
-V -pe galaxy 1</param>
          </destination>
          <destination id="sge_big" runner="sge">
            <param id="nativeSpecification">-r yes -b n -cwd -S /bin/bash
-V -pe galaxy 12</param>
          </destination>
</destinations>
<tools>
          <tool id="upload1" destination="local"/>
          <tool
id="toolshed.g2.bx.psu.edu/repos/bhaas/trinityrnaseq/trinityrnaseq/0.0.1" destination="sge_big"/>
          <tool id="mira_assembler" destination="sge_big"/>
          <tool id="megablast_wrapper" destination="sge_big"/>
          <tool
id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.1.00"
destination="sge_big"/>
          <tool
id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.1.00"
destination="sge_big"/>
          <tool
id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.1.00"
destination="sge_big"/>
          <tool
id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00"
destination="sge_big"/>
          <tool
id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.1.00"
destination="sge_big"/>
          <tool
id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpstblastn_wrapper/0.1.00"
destination="sge_big"/>
          <tool
id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpsblast_wrapper/0.1.00"
destination="sge_big"/>
</tools>
Moreover you Galaxy user and Galaxy server must be allowed to submit
jobs to your scheduler.
Hope it  helps,
Thomas
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