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titleCatch up (if needed)
Code Block
languagebash
# Copy over the Yeast data if needed
mkdir -p $SCRATCH/core_ngs/alignment/fastq
cp $CORENGS/alignment/Sample_Yeast*.gz $SCRATCH/core_ngs/alignment/fastq/

# Copy a pre-built sacCer3 reference if you didn't build one already
mkdir -p $SCRATCH/core_ngs/references
rsync -avrP $CORENGS/references/ $SCRATCH/core_ngs/references/


Code Block
languagebash
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 .
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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