>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.

Users can't control destinations for tool execution through any interface
at present AFAIK - tool destinations are automated although you can have
complex plugins which might help. One obvious if slightly painful way to
make them user selectable is to (eg) in tool_conf.xml, include a suitably
cloned version megablast for each of the two destinations - each with a new
id (eg) "megablast_local" is always sent the local queue and the
"megablast_cluster" tool always goes to the cluster in your job conf.

Ugly but possible - I hope this helps.


On Wed, Jul 16, 2014 at 5:43 PM, 王渭巍 <wangw...@inspur.com> wrote:

> 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 <thomas.bellemb...@ens-lyon.fr>
> *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
>
> --
> 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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> >
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> >
>
>
>
> ___________________________________________________________
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>
> ___________________________________________________________
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