/usr/share/doc/trimmomatic/run-unit-test is in trimmomatic 0.36+dfsg-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 | #!/bin/sh -e
pkg=trimmomatic
if [ "$ADTTMP" = "" ] ; then
ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
fi
cd $ADTTMP
cp -a /usr/share/doc/${pkg}/test_data/* .
gunzip -r *
TrimmomaticSE -phred33 test_single.fq out.fq \
ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 \
LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 \
MINLEN:36
TrimmomaticPE -phred33 test_forward.fq test_reverse.fq \
out_forward_paired.fq out_forward_unpaired.fq \
out_reverse_paired.fq out_reverse_unpaired.fq \
ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 \
TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
TrimmomaticPE -phred33 test_forward.fq test_reverse.fq \
out_forward_paired.fq out_forward_unpaired.fq \
out_reverse_paired.fq out_reverse_unpaired.fq \
ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 \
TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20
|