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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