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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