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
 
-- 
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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