Thanks, I have read tool's xml files, and I noticed that I should let the cluster run first. So I installed torque 4.2.8 in the 3 servers , and I followed https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster galaxy_user@galaxy_server% cd /clusterfs/galaxy/galaxy-dist galaxy_user@galaxy_server% LIBTORQUE_DIR=/usr/local/lib python scripts/scramble.py -e pbs_python And it seems end successfully. But then I run #sh ./run.sh in /galaxy/galaxy-dist, it comes the below error... galaxy.jobs.manager DEBUG 2014-07-16 20:03:36,159 Starting job handler galaxy.jobs.runners DEBUG 2014-07-16 20:03:36,163 Starting 4 LocalRunner workers galaxy.jobs DEBUG 2014-07-16 20:03:36,203 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' Traceback (most recent call last): File "/home/jin/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 39, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/jin/galaxy-dist/lib/galaxy/app.py", line 169, in __init__ self.job_manager = manager.JobManager( self ) File "/home/jin/galaxy-dist/lib/galaxy/jobs/manager.py", line 30, in __init__ self.job_handler = handler.JobHandler( app ) File "/home/jin/galaxy-dist/lib/galaxy/jobs/handler.py", line 29, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/home/jin/galaxy-dist/lib/galaxy/jobs/handler.py", line 567, in __init__ self.job_runners = self.app.job_config.get_job_runner_plugins() File "/home/jin/galaxy-dist/lib/galaxy/jobs/__init__.py", line 451, in get_job_runner_plugins module = __import__( module_name ) File "/home/jin/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 31, in <module> raise Exception( egg_message % str( e ) ) Exception: The 'pbs' runner depends on 'pbs_python' which is not installed or not configured properly. Galaxy's "scramble" system should make this installation simple, please follow the instructions found at: http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster Additional errors may follow: /home/jin/galaxy-dist/eggs/pbs_python-4.3.5-py2.6-linux-x86_64-ucs4.egg/_pbs.so: undefined symbol: log_record I don't know what to do again... 王渭巍 From: Thomas Bellembois Date: 2014-07-16 16:11 To: 王渭巍; galaxy-dev Subject: Re: [galaxy-dev] How to configure galaxy with a cluster 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