Question: Walltime on job_config
gravatar for David Anderson
3.8 years ago by
David Anderson40 wrote:

Hi All,


I am installing Galaxy in our HPC facility and I would like some advices regarding setting walltime for jobs in the job_config.xml.

Is there a way to know what the main Galaxy job_config looks like regarding to walltime? Specifically I would like to know what is the appropriate walltime for tools like BWA vs Blast, or even what is the recommended walltime for sort or fastQC?

I understand that this depends on the size of the dataset. But what I am looking for are just a guideline to help me set up in our own facility.


Thanks a lot


galaxy tools • 822 views
ADD COMMENTlink modified 3.8 years ago by Nate Coraor3.2k • written 3.8 years ago by David Anderson40
gravatar for Jennifer Hillman Jackson
3.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Jobs tend to fail for memory more often than wall time on the public Main Galaxy, but much depends on your own data and supported tools.

The compute given to all jobs is currently:

36 hour walltime, 6 cores, 32 GB memory, low wait

We have a beta "long running" cluster (currently not in use) with alternate configurations. These can be found here:

Other running their own servers are welcome to offer more help. Jen, Galaxy team

ADD COMMENTlink written 3.8 years ago by Jennifer Hillman Jackson25k

Thanks a lot Jennifer.

I am actually glad to know that you don't do a per tool configuration.

In our case we have a 24 cores 32GB of RAM. So I can easily emulate what you guys are doing.

But if someone else can share their config I would very much appreciate.



ADD REPLYlink written 3.8 years ago by David Anderson40
gravatar for Nate Coraor
3.8 years ago by
Nate Coraor3.2k
United States
Nate Coraor3.2k wrote:

Hi David,

The job_conf.xml for can be found here:

As Jen mentioned, we currently have a 36 hour walltime, although there are certainly jobs that could run longer - we probably set it lower than what you might do with your own resources, for quality of service purposes at the public site.

ADD COMMENTlink written 3.8 years ago by Nate Coraor3.2k

Thanks a lot Nate.
This was very helpful.

Just one more question. In the galaxy test I see that bowtie2, for example, has an option for the users choose the 'Job Resources Parameters' . 
Is this a feature that can be accomplished with the most up-to-date (stable) code or this is something not in the stable version yet? If it is possible in the stable version could you point me out to a documentation where I can learn how to do it?
I would love to give the user the chance to choose different type of queues.

Thank a lot.



ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by David Anderson40
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 171 users visited in the last hour