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Code Block
titleRun multiple alignments using the TACC batch system
# 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 . -n aln_script.cmds -t 2 -w 4 -a UT-2015-05-18 -v --reservation=CCBB
sbatch aln_script.slurm --reservation=CCBB
showq -u

While we're waiting for the job to complete, lets look at the aln_script.cmds file.