SRA-Human-Scrubber Job Scripts

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Job script used for testing application installation

#!/bin/bash
#SBATCH --job-name=sra_human_scrubber_1.1_test
#SBATCH --mail-type=NONE
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=1gb
#SBATCH --time=1:00:00
#SBATCH --output=sra_human_scrubber_1.1_test.log

echo "Setting up test environment..."
TEST_PWD=/data/apps/tests/sra_human_scrubber/1.1
TEST_DATADIR=${TEST_PWD}/example_data
TEST_WORKDIR=${TEST_PWD}/test_output

cd ${TEST_PWD}
module load sra_human_scrubber/1.1

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

echo "Starting test run at $(date) on $(hostname)..."
###################################
scrub \
    -i ${TEST_DATADIR}/scrubber_test.fastq \
    -o ${TEST_WORKDIR}/scrubber_test_clean.fastq
###################################

# There should be some files in the work directory
echo "There should be some results listed below:"
find ${TEST_WORKDIR} -type f ! -empty -ls \
&& diff ${TEST_DATADIR}/scrubber_expected_output.fastq ${TEST_WORKDIR}/scrubber_test_clean.fastq

echo "Test complete at $(date)."