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Example job script used for testing application installation
#!/bin/bash
#SBATCH --job-name=smcpp_test
#SBATCH --mail-type=NONE
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=1gb
#SBATCH --time=24:00:00
#SBATCH --output=smcpp_test.log
echo "Setting up test environment..."
TEST_PWD=/data/apps/tests/smcpp
TEST_DATADIR=${TEST_PWD}/example_data
TEST_WORKDIR=${TEST_PWD}/test_output
cd ${TEST_PWD}
module load smcpp
# Remove any previous test results and re-create a working directory
if [ -d ${TEST_WORKDIR} ]; then rm -rf ${TEST_WORKDIR}/; fi
mkdir ${TEST_WORKDIR}
cp ${TEST_DATADIR}/* ${TEST_WORKDIR}
cd ${TEST_WORKDIR}
echo "Starting test run at $(date) on $(hostname)..."
###################################
echo " Converting VCF to SMC using vcf2smc subcommand..."
smc++ \
vcf2smc \
${TEST_DATADIR}/example.vcf.gz \
${TEST_WORKDIR}/test.smc \
1 \
CEU:msp_0,msp_1
echo " Estimating using estimate subcommand..."
smc++ \
estimate \
1e-8 \
${TEST_WORKDIR}/test.smc \
-o ${TEST_WORKDIR}/output \
###################################
# There should be some files in the work directory
echo "There should be some results listed below:"
find ${TEST_WORKDIR}/output -type f ! -empty -ls
echo "Test complete at $(date)."