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#!@GNUBASH@
set -e
set -u
export SOURCE_DATE_EPOCH=1
export PIGX_UGLY=1
export PIGX_UNINSTALLED=1
# We do not use "readlink -f" here, because macos does not support it.
export srcdir=$(@PYTHON@ -c 'import os,sys; print(os.path.realpath(sys.argv[1]))' ${srcdir:-.})
chmod -R +w ${srcdir}/tests
./pigx-rnaseq -s ${srcdir}/tests/settings.yaml ${srcdir}/tests/sample_sheet.csv
if ! test -f "${srcdir}/tests/output/report/analysis1.salmon.transcripts.deseq.report.html"
then
echo "ERROR: could not find report for SALMON at transcript level"
exit 1
fi
if ! test -f "${srcdir}/tests/output/report/analysis1.salmon.genes.deseq.report.html"
then
echo "ERROR: could not find report for SALMON at gene level"
exit 1
fi
if ! test -f "${srcdir}/tests/output/report/analysis1.star.deseq.report.html"
then
echo "ERROR: could not find report for STAR"
exit 1
fi
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