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# Copy over the Yeast data if you haven't already
mkdir -p $SCRATCH/core_ngs/alignment/fastq
cp $CORENGS/alignment/*fastq.gz $SCRATCH/core_ngs/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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