Question: Galaxy Cloud @ AWS: how to use tophat2 multi-threaded?
0
gravatar for cristina.vieira
2.0 years 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 2.0 years ago by Enis Afgan670 • written 2.0 years ago by cristina.vieira0
0
gravatar for Enis Afgan
2.0 years ago by
Enis Afgan670
United States
Enis Afgan670 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 2.0 years ago by Enis Afgan670
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 136 users visited in the last hour