6 Submit bcbio job

After composing the O2.yaml configuration file, you are ready to run bcbio. Instantiate the workspace by running

bcbio_nextgen.py -w template O2.yaml alignment.csv fastq

OR, if you had merged multiple files per sample,

bcbio_nextgen.py -w template O2.yaml alignment.csv merged

You should now see the alignment/ subdirectory, and the work/ subdirectory inside of it. Descend into it:

cd alignment/work

All that remains to do is tell O2 the computational requirements for bcbio. Copy and paste the following lines into a file called submit_bcbio.sh:

#!/bin/sh
#SBATCH -p medium
#SBATCH -J bcbio_O2
#SBATCH -o run.o
#SBATCH -e run.e
#SBATCH -t 4-00:00
#SBATCH --cpus-per-task=1
#SBATCH --mem=8000

export PATH=/n/app/bcbio/tools/bin:$PATH
bcbio_nextgen.py ../config/alignment.yaml \
    -n 24 -t ipython -s slurm -q medium -r t=4-00:00 --timeout 2000

More information about these settings can be found in the O2 wiki. Once the file is ready, use it to kick off the run (after double-checking that you are currently in the alignment/work/ subdirectory):

sbatch submit_bcbio.sh