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We're going to run this script and a similar Bowtie2 alignment script, on the yeast data using the TACC batch system. In a new directory, copy over the commands and submit the batch job. We ask for 2 hours (-t 2) with 4 tasks/node (-w 4); since we have 4 commands, this will run on 1 compute node.
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| # Copy over the Yeast data |
and a pre-built reference if you haven't alreadyif needed
mkdir -p $SCRATCH/core_ngs/alignment/ |
references
rsync -avrPreferences/alignment/Sample_Yeast*.gz $SCRATCH/core_ngs/ |
referencesalignment/fastq/
# Copy a pre-built sacCer3 reference if you didn't build one already
mkdir -p $SCRATCH/core_ngs/ |
alignment/fastq
cpreferences
rsync -avrP $CORENGS/ |
alignment*fastq.gz $SCRATCH/core_ngs/references/ |
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alignment/fastq/
# Make a new alignment directory for running these scripts
mkdir -p $SCRATCH/core_ngs/alignment/bwa_script
cd $SCRATCH/core_ngs/alignment/bwa_script
ln -s -f ../fastq
# Copy the alignment commands file and submit the batch job
cp $CORENGS/tacc/aln_script.cmds .
launcher_maker.py -n aln_script.cmds -t 2 -w 4 -a UT-2015-05-18 -v --reservation=CCBB
sbatch aln_script.slurm
showq -u |
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