Hello,

I am not a megablast expert but the
"tools/metag_tools/megablast_wrapper.xml" may help you to understand how
the program is run. You may want to tune the parameters.

Regards,

Thomas

On 16/07/2014 09:43, 王渭巍 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
> 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
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