Hi Ben,
if the job is in waiting in the queue it's unlikely (not impossible)
that it is Galaxy fault. Can you recheck your Torque setup and how many
cores and memory your job has requested?
Ciao,
Bjoern
Am 22.07.2014 10:09, schrieb 王渭巍:
> Hi, Bjoern,
> I've tried the latest galaxy version with Torque 4.1.7, and it seems all right. But torque version > 4.2 won't work.
> And I tried to submit“fastqc readqc” jobs via torque (runner pbs), but the job is always in the queue waiting. I submited “fastqc readqc”local (runner local) , and the job finished successfully. So the question is , it seems not all the tools can be submitted via torque (or other resource manager), right?
>
>
>
> 王渭巍
>
> From: Björn Grüning
> Date: 2014-07-21 01:23
> To: 王渭巍; Björn Grüning; galaxy-dev
> Subject: Re: [galaxy-dev] How to configure galaxy with a cluster
> 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 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
>>> 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:
>>>
>>>
>>> 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
>>> <tool id="mira_assembler" destination="sge_big"/>
>>> <tool id="megablast_wrapper" destination="sge_big"/>
>>> <tool
>>> destination="sge_big"/>
>>> <tool
>>> destination="sge_big"/>
>>> <tool
>>> destination="sge_big"/>
>>> <tool
>>> destination="sge_big"/>
>>> <tool
>>> destination="sge_big"/>
>>> <tool
>>> destination="sge_big"/>
>>> <tool
>>> 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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