SMC++ Job Scripts

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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)."