test.sh.in

#!@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 --printshellcmds -s ${srcdir}/tests/settings.yaml ${srcdir}/tests/sample_sheet.csv

if ! test -f "${srcdir}/tests/output/report/salmon/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/salmon/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/hisat2/analysis1.deseq.report.html"
then
  echo "ERROR: could not find report for HISAT2"
  exit 1
fi