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 
> 
> 
> 
> ___________________________________________________________
> 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/
> 



___________________________________________________________
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/

Reply via email to