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
--
Thomas Bellembois, Network and System Administrator
ENS-Lyon/IGFL - FRANCE
+33 4 26 73 13 67
.The IGFL is a member of the "portail-labos" project
(https://portail-labos.ens-lyon.fr/site/).
.IGFL IT documentation: http://itdoc.igfl.ens-lyon.fr/itdoc
On 15/07/2014 11:22, 王渭巍 wrote:
> Hello, everyone,
> I am new here, and I am trying to configure galaxy with a cluster.
> I have 3 servers. One for galaxy server, two for cluster computing. And I followed "Running Galaxy Tools on a Cluster" done the configuration.
> Now I have 2 questions:
> 1. How to vertify whether I have configured the galaxy cluster successfully? For example, I don't see there is any cluster options in "NGS mapping (bowtie2) ", but I see cluster options in a web galaxy.
> 2. And any other work I should do for configuring galaxy with a cluster?
> Thank you for any help.
>
> Ben
>
>
>
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