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ewels / clusterflow

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.
https://ewels.github.io/clusterflow/
GNU General Public License v3.0
97 stars 27 forks source link

Add HPC option for local machine #34

Closed ewels closed 9 years ago

ewels commented 9 years ago

Would be nice to be able to run pipelines locally instead of having to always submit jobs to the cluster.

Could perhaps write a bash file with the commands, in order. Then submit:

nohup bash cf_commands.sh &
ewels commented 9 years ago

Would be nice to add in --qstat and --qdel for local.

For --qdel:

ps fu | grep cf_local_cf # Or something more clever to get $PID
kill -9 -$(ps -o pgid= $PID | grep -o '[0-9]*')

Kill command from here

ewels commented 9 years ago

Aha, pgrep seems to be the chap here. Would be nice to read the bash file as well, then look at child processes to figure out what step number we're on for --qstat

ewels commented 9 years ago

Add #!/bin/bash to script and some comments saying what it is and when it was created...