RMATS-turbo Job Scripts

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Job script used for testing application installation:

#!/bin/bash
#SBATCH --job-name=rmats-turbo_test
#SBATCH --mail-type=NONE
#SBATCH --cpus-per-task=32
#SBATCH --mem-per-cpu=4gb
#SBATCH --time=24:00:00
#SBATCH --output=rmats-turbo_test.log

echo "Setting up test environment..."
TEST_PWD=/data/apps/tests/rmats-turbo
TEST_DATADIR=${TEST_PWD}/example_data
TEST_OUTDIR=${TEST_PWD}/test_output
TEST_WORKDIR=${TEST_PWD}/tmp

cd ${TEST_PWD}
module load rmats-turbo

# Remove any previous test results and re-create a working directory
if [ -d ${TEST_OUTDIR} ]; then rm -rf ${TEST_OUTDIR}/; fi
mkdir ${TEST_OUTDIR}

if [ -d ${TEST_WORKDIR} ]; then rm -rf ${TEST_WORKDIR}/; fi
mkdir ${TEST_WORKDIR}

# The fasta file must be in the current directory becasue the invoked
# STAR command does not use absolute paths...
cp ${TEST_DATADIR}/* ${TEST_PWD}

echo "Starting test run at $(date) on $(hostname)..."

###################################
# Example built from:
#    https://github.com/Xinglab/rmats-turbo#starting-with-fastq-files

run_rmats \
    --s1 s1.txt \
    --s2 s2.txt \
    --gtf /data/reference/gtf/Homo_sapiens.knownGene.hg19.gtf \
    --bi /data/reference/star/2.7/hg19 \
    --readLength 50 \
    --nthread ${SLURM_CPUS_PER_TASK:-4} \
    --od ${TEST_OUTDIR} \
    --tmp ${TEST_WORKDIR}

###################################

# There should be some files in the work directory
echo "There should be some results listed below:"
find ${TEST_OUTDIR} -type f ! -empty -ls

echo "Test complete at $(date)."