/
run_test.sh
executable file
·63 lines (53 loc) · 1.74 KB
/
run_test.sh
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#! /bin/bash
set -e
! getopt --test > /dev/null
if [[ ${PIPESTATUS[0]} -ne 4 ]]; then
echo 'I am sorry, $(getopt --test) failed in this environment.'
exit 1
fi
OPTIONS=d:
LONGOPTIONS=dataset:
if [[ ${PIPESTATUS[0]} -ne 0 ]]; then
# e.g. return value is 1
# then getopt has complained about wrong arguments to stdout
exit 2
fi
d=-
if [ $# -lt 2 ]; then
echo "Usage: run_test.sh [-d | --dataset] DATASET [-h | --help]"
exit 1
fi
while [[ "$#" -gt 0 ]]; do
case $1 in
-d|--dataset)
dataset="$2"
shift
;;
-h|--help)
echo "Usage: run_test.sh [-d | --dataset] DATASET [-h | --help]"
exit 1
;;
*)
echo "Unknown parameter passed to $1"
exit 3
;;
esac
shift
done
TEST_DATA_DIR=test/data/${dataset}
RUN_DATA_DIR=/tmp/rarefan_test
RUN_OUT_DIR=${RUN_DATA_DIR}/out
rsync -ruvL ${TEST_DATA_DIR}/ ${RUN_DATA_DIR}/
rsync -uv test/data/yafM_Ecoli.faa ${RUN_DATA_DIR}
rsync -uv test/data/yafM_SBW25.faa ${RUN_DATA_DIR}
if [[ ! $dataset == *"chlororaphis"* ]]; then
treename="tmptree"
java -Xmx10g -jar REPIN_ecology/REPIN_ecology/build/libs/REPIN_ecology.jar ${RUN_DATA_DIR} ${RUN_OUT_DIR} Nmen_2594.fas 55 21 ${RUN_DATA_DIR}/yafM_Ecoli.faa ${treename}.nwk 1e-30 true
fi
if [[ $dataset == *"chlororaphis"* ]]; then
treename="chlororaphis"
RUN_OUT_DIR=${RUN_DATA_DIR}/test_out
java -Xmx10g -jar REPIN_ecology/REPIN_ecology/build/libs/REPIN_ecology.jar ${RUN_DATA_DIR}/in ${RUN_OUT_DIR} chlTAMOak81.fas 55 21 ${RUN_DATA_DIR}/yafM_SBW25.faa ${treename}.nwk 1e-30 true
fi
andi ${RUN_DATA_DIR}/*.fas > ${RUN_OUT_DIR}/${treename}.dist
clustDist ${RUN_OUT_DIR}/${treename}.dist > ${RUN_OUT_DIR}/${treename}.nwk