=========================================================== .___ __ __ _________________ __ __ __| _/|__|/ |_ / ___\_` __ \__ \ | | \/ __ | | \\_ __\ / /_/ > | \// __ \| | / /_/ | | || | \___ /|__| (____ /____/\____ | |__||__| /_____/ \/ \/ grep rough audit - static analysis tool v2.8 written by @Wireghoul =================================[justanotherhacker.com]=== trim-galore-0.6.6/Changelog.md-48- trim-galore-0.6.6/Changelog.md:49:- Fixed setting `-j $cores` for Cutadapt versions 2.X or above. trim-galore-0.6.6/Changelog.md-50- ############################################## trim-galore-0.6.6/trim_galore-1473- if ($fastqc_args){ trim-galore-0.6.6/trim_galore:1474: system ("$path_to_fastqc $fastqc_args $output_dir$output_filename"); trim-galore-0.6.6/trim_galore-1475- } trim-galore-0.6.6/trim_galore-1476- else{ trim-galore-0.6.6/trim_galore:1477: system ("$path_to_fastqc $output_dir$output_filename"); trim-galore-0.6.6/trim_galore-1478- } ############################################## trim-galore-0.6.6/trim_galore-1524- if ($fastqc_args){ trim-galore-0.6.6/trim_galore:1525: system ("$path_to_fastqc $fastqc_args $output_dir$val_1"); trim-galore-0.6.6/trim_galore-1526- } trim-galore-0.6.6/trim_galore-1527- else{ trim-galore-0.6.6/trim_galore:1528: system ("$path_to_fastqc $output_dir$val_1"); trim-galore-0.6.6/trim_galore-1529- } ############################################## trim-galore-0.6.6/trim_galore-1534- if ($fastqc_args){ trim-galore-0.6.6/trim_galore:1535: system ("$path_to_fastqc $fastqc_args $output_dir$val_2"); trim-galore-0.6.6/trim_galore-1536- } trim-galore-0.6.6/trim_galore-1537- else{ trim-galore-0.6.6/trim_galore:1538: system ("$path_to_fastqc $output_dir$val_2"); trim-galore-0.6.6/trim_galore-1539- } ############################################## trim-galore-0.6.6/trim_galore-2491- warn "Cutadapt seems to be working fine (tested command '$path_to_cutadapt --version')\n"; trim-galore-0.6.6/trim_galore:2492: $cutadapt_version = `$path_to_cutadapt --version 2>&1`; trim-galore-0.6.6/trim_galore-2493- chomp $cutadapt_version; ############################################## trim-galore-0.6.6/trim_galore-2507- # warn "Let's also find out the Python version used. $path_to_cutadapt\n"; trim-galore-0.6.6/trim_galore:2508: my $location_of_cutadapt = `which $path_to_cutadapt`; trim-galore-0.6.6/trim_galore-2509- #warn "Location is: $location_of_cutadapt\n"; ############################################## trim-galore-0.6.6/trim_galore-2525- trim-galore-0.6.6/trim_galore:2526: my $python_return = `$shebang --version 2>&1`; trim-galore-0.6.6/trim_galore-2527- chomp $python_return; ############################################## trim-galore-0.6.6/debian/createmanpages-4- trim-galore-0.6.6/debian/createmanpages:5:VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'` trim-galore-0.6.6/debian/createmanpages-6-NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1` ############################################## trim-galore-0.6.6/debian/tests/run-unit-test-6-if [ "$AUTOPKGTEST_TMP" = "" ] ; then trim-galore-0.6.6/debian/tests/run-unit-test:7: AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX` trim-galore-0.6.6/debian/tests/run-unit-test-8- trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM