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commit 3ec2633dbb17cf0cba2e4707695224ef952c2c7b Author: Andreas Tille <[email protected]> Date: Wed Feb 22 17:18:19 2017 +0100 Somehow also test bwa - not finished --- debian/tests/bwa/run.sh | 89 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 89 insertions(+) diff --git a/debian/tests/bwa/run.sh b/debian/tests/bwa/run.sh new file mode 100644 index 0000000..924228f --- /dev/null +++ b/debian/tests/bwa/run.sh @@ -0,0 +1,89 @@ +#!/bin/bash +# this is a rough edit of upstreams tests/bwa/run.sh to make +# it somehow working. It definitely needs more care (FIXME!) +# to make it a real test + +set -o nounset # Fail on unset variables +set -o errexit # Fail on uncaught non-zero returncodes +set -o pipefail # Fail is a command in a chain of pipes fails + +echo cd $(dirname $0) + +# Errors to ignore during valiation +IGNORE="IGNORE=RECORD_MISSING_READ_GROUP IGNORE=MISSING_READ_GROUP" + +ls -d testcases/* | +while read testcase; +do + echo "Running testcase ${testcase}: $(head -n1 ${testcase}/README)" + mkdir -p debian + ln -sf /usr/bin/bwa debian + readlink debian/bwa | + while read BWA; + do + echo -n " $BWA " + + rm -rf temp + folder="runs/$testcase/$(dirname $BWA | xargs basename)" + rm -rf $folder + mkdir -p $folder + ln -s $folder temp + + msg="" + returncode=-1 + + cp ${testcase}/* temp/ + if [ -e "temp/run.sh" ]; + then + bash "temp/run.sh" "/usr/bin/bwa" && returncode=$? || returncode=$? + + if [ -e "temp/run.log" ]; + then + msg="$(head -n1 temp/run.log)" + fi + elif [ -e "temp/reads1.fasta" ]; + then + PREFIX=temp/prefix.fasta + READS1=temp/reads1.fasta + READS2=temp/reads2.fasta + RESULTS=temp/results + + command="index" + if $BWA index ${PREFIX} 2> ${PREFIX}.log; + then + command="aln #1" + if $BWA aln ${PREFIX} ${READS1} > ${READS1}.fai 2> ${READS1}.log; + then + command="aln #2" + if $BWA aln ${PREFIX} ${READS2} > ${READS2}.fai 2> ${READS2}.log; + then + command="sampe" + if $BWA sampe ${PREFIX} ${READS1}.fai ${READS2}.fai ${READS1} ${READS2} 2> ${RESULTS}.log | \ + paleomix cleanup --paired --fasta ${PREFIX} --temp-prefix temp/cleanup 2> ${RESULTS}.cleanup.log > ${RESULTS}.bam; + then + java -jar "ValidateSamFile.jar" ${IGNORE} I=${RESULTS}.bam &> ${RESULTS}.bam.validated \ + && returncode=$? || returncode=$? + + if [ -e "${RESULTS}.bam.validated" ]; + then + msg="$((grep ERROR ${RESULTS}.bam.validated || true) | head -n1)" + fi + fi + fi + fi + fi + fi + + if test $returncode -eq 0; + then + echo -e "\033[32m[OK]\033[0m" + elif test $returncode -eq -1; + then + echo -e "\033[31m[TEST ERROR]: $command\033[0m" + else + echo -e "\033[33m[FAILED]\033[0m: $msg" + fi + done +done + +rm -rf temp -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/paleomix.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
