Question: Galaxy Cloud @ AWS: how to use tophat2 multi-threaded?
0
gravatar for cristina.vieira
21 months ago by
cristina.vieira0 wrote:

I'm trying to run tophat2 job on my cluster, having allocated 32 core worker node expecting some parallelisation. When I connect to the node and issue "top" I see "bowie-2-align-s" process running for 30min on a single core/thread.

What do I have to do to make the job run multi-threaded ?

This is the command sent by galaxy to run the task: "tophat2 --num-threads ${GALAXY_SLOTS:-4} --read-mismatches 2 ..."

Thx

ADD COMMENTlink modified 21 months ago by Enis Afgan620 • written 21 months ago by cristina.vieira0
0
gravatar for Enis Afgan
21 months ago by
Enis Afgan620
United States
Enis Afgan620 wrote:

There's a good discussion about setting up a specific tool to run using multiple cores available here: http://dev.list.galaxyproject.org/quot-GALAXY-SLOTS-4-quot-usage-help-td4669264.html. Hopefully that can help but if you have more questions about the setup details, feel free to post those here.

ADD COMMENTlink written 21 months ago by Enis Afgan620
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