PGAP Job Scripts

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Script used to test application installation

#!/bin/bash
#SBATCH --job-name=pgap_20220414_test
#SBATCH --mail-type=NONE
#SBATCH --cpus-per-task=28
#SBATCH --mem-per-cpu=4gb
#SBATCH --time=24:00:00
#SBATCH --output=pgap_20220414_test.log

echo "Setting up test environment..."
TEST_PWD=/data/apps/tests/pgap/20220414
TEST_DATADIR=${TEST_PWD}/example_data
TEST_WORKDIR=${TEST_PWD}/test_output

cd ${TEST_PWD}
module load pgap/20220414

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

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

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

pgap.py \
    --cpus ${SLURM_CPUS_ON_NODE:-4} \
    -o ${TEST_WORKDIR} \
    ${HPC_PGAP_DIR}/test_genomes/MG37/input.yaml

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

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

echo "Test complete at $(date)."