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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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

Hi Ben, that is not possible at the moment. The idea is to keep the user-inferface as easy as possible for the user. You, as admin, can decide which resource a specific tool with a specific input will use. You will never see any options like that in a tool, but you can write a tool by yourself if you like, or "enhance" the megablast tool. Cheers, Bjoern Am 16.07.2014 09:43, schrieb 王渭巍:

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

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

Hi Ben, sorry but we do not run a Torque setup. Do you have any concrete questions or error messages? Cheers, Bjoern Am 17.07.2014 04:10, schrieb 王渭巍:

Hi, Bjoern Would you share your procedure to make some tools to run on a cluster. I have tried https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster using Torque, but got errors. I think maybe it's job_conf.xml. Would you share yours? Thanks a lot

Ben

From: Björn Grüning Date: 2014-07-16 16:34 To: 王渭巍; Thomas Bellembois; galaxy-dev Subject: Re: [galaxy-dev] How to configure galaxy with a cluster Hi Ben,

that is not possible at the moment. The idea is to keep the user-inferface as easy as possible for the user. You, as admin, can decide which resource a specific tool with a specific input will use. You will never see any options like that in a tool, but you can write a tool by yourself if you like, or "enhance" the megablast tool.

Cheers, Bjoern

Am 16.07.2014 09:43, schrieb 王渭巍:

...

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

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

Hi Ben, if the job is in waiting in the queue it's unlikely (not impossible) that it is Galaxy fault. Can you recheck your Torque setup and how many cores and memory your job has requested? Ciao, Bjoern Am 22.07.2014 10:09, schrieb 王渭巍:

Hi, Bjoern, I've tried the latest galaxy version with Torque 4.1.7, and it seems all right. But torque version > 4.2 won't work. And I tried to submit“fastqc readqc” jobs via torque (runner pbs), but the job is always in the queue waiting. I submited “fastqc readqc”local (runner local) , and the job finished successfully. So the question is , it seems not all the tools can be submitted via torque (or other resource manager), right?

王渭巍

From: Björn Grüning Date: 2014-07-21 01:23 To: 王渭巍; Björn Grüning; galaxy-dev Subject: Re: [galaxy-dev] How to configure galaxy with a cluster Hi Ben,

sorry but we do not run a Torque setup.

Do you have any concrete questions or error messages?

Cheers, Bjoern

Am 17.07.2014 04:10, schrieb 王渭巍:

...

Hi, Bjoern Would you share your procedure to make some tools to run on a cluster. I have tried https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster using Torque, but got errors. I think maybe it's job_conf.xml. Would you share yours? Thanks a lot

Ben

From: Björn Grüning Date: 2014-07-16 16:34 To: 王渭巍; Thomas Bellembois; galaxy-dev Subject: Re: [galaxy-dev] How to configure galaxy with a cluster Hi Ben,

that is not possible at the moment. The idea is to keep the user-inferface as easy as possible for the user. You, as admin, can decide which resource a specific tool with a specific input will use. You will never see any options like that in a tool, but you can write a tool by yourself if you like, or "enhance" the megablast tool.

Cheers, Bjoern

Am 16.07.2014 09:43, schrieb 王渭巍:

...

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

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

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Hi Ben, Most of the tools you are looking for should be in the Galaxy Tool Shed: https://toolshed.g2.bx.psu.edu/ As for the earlier question regarding the resource selector drop down menu which I assume you are seeing on Galaxy Test, this is a feature currently available in the development version of Galaxy, and will be part of the next stable release: https://bitbucket.org/galaxy/galaxy-central/commits/31b2924315d0b48fa7648ab4... --nate On Jul 24, 2014, at 6:08 AM, 王渭巍 <wangweiw@inspur.com> wrote:

Thank you, Bjoern It turns out that I forgot start the scheduler, and now galaxy runs smoothly with torque. I am also trying to add more tools, some .xml config of the added tools can be found in "tools", but some of them are missing, I don't know where are they. I want to try do some customizing to the web interface of the tools. Is there any guidline for me? Thanks a lot.

Ciao, Ben

From: Björn Grüning Date: 2014-07-22 16:15 To: 王渭巍; Björn Grüning; galaxy-dev Subject: Re: [galaxy-dev] How to configure galaxy with a cluster Hi Ben,

if the job is in waiting in the queue it's unlikely (not impossible) that it is Galaxy fault. Can you recheck your Torque setup and how many cores and memory your job has requested?

Ciao, Bjoern

Am 22.07.2014 10:09, schrieb 王渭巍:

...

Hi, Bjoern, I've tried the latest galaxy version with Torque 4.1.7, and it seems all right. But torque version > 4.2 won't work. And I tried to submit“fastqc readqc” jobs via torque (runner pbs), but the job is always in the queue waiting. I submited “fastqc readqc”local (runner local) , and the job finished successfully. So the question is , it seems not all the tools can be submitted via torque (or other resource manager), right?

王渭巍

From: Björn Grüning Date: 2014-07-21 01:23 To: 王渭巍; Björn Grüning; galaxy-dev Subject: Re: [galaxy-dev] How to configure galaxy with a cluster Hi Ben,

sorry but we do not run a Torque setup.

Do you have any concrete questions or error messages?

Cheers, Bjoern

Am 17.07.2014 04:10, schrieb 王渭巍:

...

Hi, Bjoern Would you share your procedure to make some tools to run on a cluster. I have tried https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster using Torque, but got errors. I think maybe it's job_conf.xml. Would you share yours? Thanks a lot

Ben

From: Björn Grüning Date: 2014-07-16 16:34 To: 王渭巍; Thomas Bellembois; galaxy-dev Subject: Re: [galaxy-dev] How to configure galaxy with a cluster Hi Ben,

that is not possible at the moment. The idea is to keep the user-inferface as easy as possible for the user. You, as admin, can decide which resource a specific tool with a specific input will use. You will never see any options like that in a tool, but you can write a tool by yourself if you like, or "enhance" the megablast tool.

Cheers, Bjoern

Am 16.07.2014 09:43, schrieb 王渭巍:

...

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

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