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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