Question: Galaxy on a Centos Cluster + SLURM: how to configure runners?
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gravatar for clijeron
2.2 years ago by
clijeron10
United States
clijeron10 wrote:

Is there any guideline on how to setup an instance of Galaxy running on a cluster that uses SLURM as the workload manager?  Since I'm a newbie in Linux administration there are many things that are not clear from the Galaxy project website; I feel some steps are omitted, or I'm not getting a clear picture.

This is what I've done so far:

  1. Installed the latest version of Galaxy pulled from Github.  This installation is on the head node
  2. Installed and setup MySQL to work with Galaxy
  3. Installed drmaa-python library to connect Galaxy and SLURM

 

From this point on I'm stuck and I don't know how Galaxy can make use of the cluster.  I have a dedicated partition for use by Galaxy jobs.   Please advise.

 

BTW: Our OS is Centos 6.5

 

Thank you.

Carlos.

 

slurm drmaa-python cluster • 990 views
ADD COMMENTlink written 2.2 years ago by clijeron10

Hi Carlos

This is not an answer to your question, but rather an advice: Since you are starting a new Galaxy installation, I strongly recommend to use PostgreSQL rather than MySQL. PostgreSQL is the preferred database server by the Galaxy team.

Regards, Hans-Rudolf

ADD REPLYlink written 2.2 years ago by Hotz, Hans-Rudolf1.7k

Hans,

Thank you for the advise on PostgreSQL. I believe that if we use the InnoDB storage engine we can get a reliable database service on MySQL to support Galaxy as robust as PostgreSQL. Does anyone have any bad experience with MySQL or addition consideration we need to take? We are in our early deployment stage, therefore these tips are very valuable. Thanks again !

Carlos.

From: "Hotz, Hans-Rudolf on Galaxy Biostar" <notifications@biostars.org<mailto:notifications@biostars.org>> Reply-To: "galaxystar+b4106fff+code@biostars.io<mailto:galaxystar+b4106fff+code@biostars.io>" <galaxystar+b4106fff+code@biostars.io<mailto:galaxystar+b4106fff+code@biostars.io>> Date: Tuesday, September 22, 2015 at 7:41 AM To: Carlos Lijeron <clijeron@hunter.cuny.edu<mailto:clijeron@hunter.cuny.edu>> Subject: [galaxy-biostar] C: Galaxy on a Centos Cluster + SLURM: how to configure runners?

Activity on a post you are following on Galaxy Biostar<http: biostar.usegalaxy.org="">

User Hotz, Hans-Rudolf<http: biostar.usegalaxy.org="" u="" 179=""/> wrote Comment: Galaxy on a Centos Cluster + SLURM: how to configure runners?<http: biostar.usegalaxy.org="" p="" 14264="" #14275="">:

Hi Carlos

This is not an answer to your question, but rather an advice: Since you are starting a new Galaxy installation, I strongly recommend to use PostgreSQL rather than MySQL. PostgreSQL is the preferred database server by the Galaxy team.

Regards, Hans-Rudolf

ADD REPLYlink written 2.2 years ago by clijeron10
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