>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 <wangweiw@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


 
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
 
--
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
.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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