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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
raxml-8.2.12+dfsg/usefulScripts/ProteinModelSelection.pl-61- $cmd = $raxmlExecutable." -f s -m PROTCATJTT -p 12345 -s ".$alignmentName." -q ".$partition." -n SPLIT_".$alignmentName." \> SPLIT_".$alignmentName."_out";
raxml-8.2.12+dfsg/usefulScripts/ProteinModelSelection.pl:62: system($cmd);
raxml-8.2.12+dfsg/usefulScripts/ProteinModelSelection.pl-63- $count = 0;
##############################################
raxml-8.2.12+dfsg/usefulScripts/ProteinModelSelection.pl-68- #print "perl ProteinModelSelection.pl ".$alignmentName.".GENE.".$count;
raxml-8.2.12+dfsg/usefulScripts/ProteinModelSelection.pl:69: system("perl ProteinModelSelection.pl ".$alignmentName.".GENE.".$count);
raxml-8.2.12+dfsg/usefulScripts/ProteinModelSelection.pl-70- $count = $count + 1;
##############################################
raxml-8.2.12+dfsg/usefulScripts/ProteinModelSelection.pl-77- $cmd = $raxmlExecutable." -y -p 12345 -m PROTCATJTT -s ".$alignmentName." -n ST_".$alignmentName." \> ST_".$alignmentName."_out";
raxml-8.2.12+dfsg/usefulScripts/ProteinModelSelection.pl:78: system($cmd);
raxml-8.2.12+dfsg/usefulScripts/ProteinModelSelection.pl-79-
##############################################
raxml-8.2.12+dfsg/usefulScripts/ProteinModelSelection.pl-86- #print($cmd);
raxml-8.2.12+dfsg/usefulScripts/ProteinModelSelection.pl:87: system($cmd);
raxml-8.2.12+dfsg/usefulScripts/ProteinModelSelection.pl-88- }
##############################################
raxml-8.2.12+dfsg/usefulScripts/applyRAxML2AllFilesInDirectory.pl-38- print "$cmd";
raxml-8.2.12+dfsg/usefulScripts/applyRAxML2AllFilesInDirectory.pl:39: system($cmd);
raxml-8.2.12+dfsg/usefulScripts/applyRAxML2AllFilesInDirectory.pl-40- }
##############################################
raxml-8.2.12+dfsg/usefulScripts/bsBranchLengths.pl-16-
raxml-8.2.12+dfsg/usefulScripts/bsBranchLengths.pl:17:system("./raxmlHPC -f j -m GTRCAT -b 12345 -# ".$reps." -s ".$alignment." -n REPLICATES");
raxml-8.2.12+dfsg/usefulScripts/bsBranchLengths.pl-18-
##############################################
raxml-8.2.12+dfsg/usefulScripts/bsBranchLengths.pl-21- {
raxml-8.2.12+dfsg/usefulScripts/bsBranchLengths.pl:22: system("./raxmlHPC -f e -m GTRGAMMA -t ".$tree." -s ".$alignment.".BS".$i." -n REP".$i);
raxml-8.2.12+dfsg/usefulScripts/bsBranchLengths.pl-23- }
##############################################
raxml-8.2.12+dfsg/usefulScripts/bsBranchLengths.pl-31-
raxml-8.2.12+dfsg/usefulScripts/bsBranchLengths.pl:32:system("cat ".$concat." > bsTrees");
raxml-8.2.12+dfsg/usefulScripts/bsBranchLengths.pl-33-
##############################################
raxml-8.2.12+dfsg/debian/createmanpages-4-
raxml-8.2.12+dfsg/debian/createmanpages:5:VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
raxml-8.2.12+dfsg/debian/createmanpages-6-NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
##############################################
raxml-8.2.12+dfsg/debian/rules-34- dh_auto_build --buildsystem=makefile -- -f $${mfile} $(MFLAGS); \
raxml-8.2.12+dfsg/debian/rules:35: curexe=`ls $(exe)* | head -n 1` ; \
raxml-8.2.12+dfsg/debian/rules-36- if [ -e $(BINDIR)/$${curexe} ] ; then \
##############################################
raxml-8.2.12+dfsg/debian/rules-53- dh_installman
raxml-8.2.12+dfsg/debian/rules:54: for cexe in `ls $(BINDIR)/$(exe)*` ; do \
raxml-8.2.12+dfsg/debian/rules:55: curexe=`basename $${cexe}` ; \
raxml-8.2.12+dfsg/debian/rules-56- if [ $${curexe} != $(exe) ] ; then \
##############################################
raxml-8.2.12+dfsg/debian/rules-64- for pscript in `ls usefulScripts/*.pl` ; do \
raxml-8.2.12+dfsg/debian/rules:65: sed 's?/usr/local/bin/perl?/usr/bin/perl?' $${pscript} > $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/examples/`basename $${pscript}` ; \
raxml-8.2.12+dfsg/debian/rules-66- done