comparison pal_finder_wrapper.sh @ 7:5e133b7b79a6 draft

Uploaded version 0.02.04.6 (uses conda dependency resolution).

6:a73c48890bde

if [ -z "$(tail -n 1 pal_finder.log | grep Done!!)" ] ; then
    echo ERROR pal_finder failed to complete successfully >&2
    exit 1
fi
#
# Sort outputs into a consistent order regardless of Perl version
echo "### Sorting outputs ###"
head -1 Output/PAL_summary.txt > Output/PAL_summary.sorted.txt
if [ "$PLATFORM" == "Illumina" ] ; then
    grep -v "^readPairID" Output/PAL_summary.txt | sort -k 1 >> Output/PAL_summary.sorted.txt
else
    grep -v "^SequenceID" Output/PAL_summary.txt | sort -k 1 >> Output/PAL_summary.sorted.txt

7:5e133b7b79a6

if [ -z "$(tail -n 1 pal_finder.log | grep Done!!)" ] ; then
    echo ERROR pal_finder failed to complete successfully >&2
    exit 1
fi
#
# Sort microsat_summary output
echo "### Sorting microsat summary output ###"
head -n 7 Output/microsat_summary.txt | sort >microsat_summary.sorted
grep "^$" Output/microsat_summary.txt>>microsat_summary.sorted
grep "^Microsat Type" Output/microsat_summary.txt >>microsat_summary.sorted
tail -n +11 Output/microsat_summary.txt >>microsat_summary.sorted
mv microsat_summary.sorted Output/microsat_summary.txt
#
# Sort PAL_summary output
echo "### Sorting PAL summary output ###"
head -1 Output/PAL_summary.txt > Output/PAL_summary.sorted.txt
if [ "$PLATFORM" == "Illumina" ] ; then
    grep -v "^readPairID" Output/PAL_summary.txt | sort -k 1 >> Output/PAL_summary.sorted.txt
else
    grep -v "^SequenceID" Output/PAL_summary.txt | sort -k 1 >> Output/PAL_summary.sorted.txt