===========================================================
.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
gbrowse-2.56+dfsg/bin/bp_load_gff.pl-95- 'quiet' => \$QUIET,
gbrowse-2.56+dfsg/bin/bp_load_gff.pl:96: create => \$CREATE) or (system('pod2text',$0), exit -1);
gbrowse-2.56+dfsg/bin/bp_load_gff.pl-97-
##############################################
gbrowse-2.56+dfsg/bin/gbrowse_netinstall.pl-253- # my $bioperl_index = find_bioperl_ppm();
gbrowse-2.56+dfsg/bin/gbrowse_netinstall.pl:254: # system("ppm install --force $bioperl_index");
gbrowse-2.56+dfsg/bin/gbrowse_netinstall.pl-255- #} else {
##############################################
gbrowse-2.56+dfsg/bin/gbrowse_netinstall.pl-327- if ($method eq 'make') {
gbrowse-2.56+dfsg/bin/gbrowse_netinstall.pl:328: system("$perl_path Makefile.PL $build_param_string") == 0
gbrowse-2.56+dfsg/bin/gbrowse_netinstall.pl-329- or die "Couldn't run perl Makefile.PL command\n";
gbrowse-2.56+dfsg/bin/gbrowse_netinstall.pl:330: system("$make install UNINST=1 $install_param_string") == 0 ;
gbrowse-2.56+dfsg/bin/gbrowse_netinstall.pl-331- }
gbrowse-2.56+dfsg/bin/gbrowse_netinstall.pl-332- elsif ($method eq 'Build') {
gbrowse-2.56+dfsg/bin/gbrowse_netinstall.pl:333: system("$perl_path $build_str.PL --yes=1") == 0
gbrowse-2.56+dfsg/bin/gbrowse_netinstall.pl-334- or die "Couldn't run perl Build.PL command\n";
gbrowse-2.56+dfsg/bin/gbrowse_netinstall.pl:335: system("$build_str install --uninst 1") == 0;
gbrowse-2.56+dfsg/bin/gbrowse_netinstall.pl-336- }
##############################################
gbrowse-2.56+dfsg/bin/gbrowse_netinstall.pl-458- next if $repository{$name};
gbrowse-2.56+dfsg/bin/gbrowse_netinstall.pl:459: system("ppm rep add $name $REPOSITORIES{$name}");
gbrowse-2.56+dfsg/bin/gbrowse_netinstall.pl-460- }
##############################################
gbrowse-2.56+dfsg/bin/gbrowse_netinstall2.pl-222- my $bioperl_index = find_bioperl_ppm();
gbrowse-2.56+dfsg/bin/gbrowse_netinstall2.pl:223: system("ppm install --force $bioperl_index");
gbrowse-2.56+dfsg/bin/gbrowse_netinstall2.pl-224- } else {
##############################################
gbrowse-2.56+dfsg/bin/gbrowse_netinstall2.pl-272- if ($method eq 'make') {
gbrowse-2.56+dfsg/bin/gbrowse_netinstall2.pl:273: system("perl Makefile.PL $build_param_string") == 0
gbrowse-2.56+dfsg/bin/gbrowse_netinstall2.pl-274- or die "Couldn't run perl Makefile.PL command\n";
gbrowse-2.56+dfsg/bin/gbrowse_netinstall2.pl:275: system("$make install UNINST=1 $install_param_string") == 0 ;
gbrowse-2.56+dfsg/bin/gbrowse_netinstall2.pl-276- }
gbrowse-2.56+dfsg/bin/gbrowse_netinstall2.pl-277- elsif ($method eq 'Build') {
gbrowse-2.56+dfsg/bin/gbrowse_netinstall2.pl:278: system("perl $build_str.PL --yes=1") == 0
gbrowse-2.56+dfsg/bin/gbrowse_netinstall2.pl-279- or die "Couldn't run perl Build.PL command\n";
gbrowse-2.56+dfsg/bin/gbrowse_netinstall2.pl:280: system("$build_str install --uninst 1") == 0;
gbrowse-2.56+dfsg/bin/gbrowse_netinstall2.pl-281- }
##############################################
gbrowse-2.56+dfsg/bin/gbrowse_netinstall2.pl-399- next if $repository{$name};
gbrowse-2.56+dfsg/bin/gbrowse_netinstall2.pl:400: system("ppm rep add $name $REPOSITORIES{$name}");
gbrowse-2.56+dfsg/bin/gbrowse_netinstall2.pl-401- }
##############################################
gbrowse-2.56+dfsg/bin/process_ncbi_human.pl-122- #Is this an argstring or file with the string in it?
gbrowse-2.56+dfsg/bin/process_ncbi_human.pl:123: my $dbistring = -f $doTSCSNP ? `cat $doTSCSNP` : $doTSCSNP;
gbrowse-2.56+dfsg/bin/process_ncbi_human.pl-124- $dbh = &dbConnect($dbistring);
##############################################
gbrowse-2.56+dfsg/bin/split_wig.pl-38-my $out=File::Temp->new(DIR => $dir, UNLINK => 0, SUFFIX => '.dat');
gbrowse-2.56+dfsg/bin/split_wig.pl:39:my $header=`head -n 1 $wig`;
gbrowse-2.56+dfsg/bin/split_wig.pl-40-open IN, $wig or die "Cannot open $wig: $!\n";
##############################################
gbrowse-2.56+dfsg/bin/split_wig.pl-68- my $outfile="$path/gff3_files/$filename[0]_$suf.gff3";
gbrowse-2.56+dfsg/bin/split_wig.pl:69: system("wiggle2gff3.pl --path=$path/wib_files $_ > $tmpout");
gbrowse-2.56+dfsg/bin/split_wig.pl:70: system ("sed 's/microarray_oligo/$filename[0]/' $tmpout > $outfile");
gbrowse-2.56+dfsg/bin/split_wig.pl-71- $suf++;
##############################################
gbrowse-2.56+dfsg/bin/gbrowse_metadb_config.pl-311- $settings->{uploadid};
gbrowse-2.56+dfsg/bin/gbrowse_metadb_config.pl:312: $database->do("UPDATE session SET uploadsid = ? WHERE sessionid = ?", undef, $uploadsid, $userid) or print STDERR "could not add to database.\n" . DBI->errstr;
gbrowse-2.56+dfsg/bin/gbrowse_metadb_config.pl-313- print STDERR "added to database.\n" unless DBI->errstr;
##############################################
gbrowse-2.56+dfsg/bin/gbrowse_metadb_config.pl-371- foreach my $file (@files) {
gbrowse-2.56+dfsg/bin/gbrowse_metadb_config.pl:372: my @data_source_in_db = $database->selectrow_array("SELECT data_source FROM uploads WHERE path = ? AND userid = ?", undef, $file, $uploadsid);
gbrowse-2.56+dfsg/bin/gbrowse_metadb_config.pl-373- unless (@data_source_in_db) {
##############################################
gbrowse-2.56+dfsg/bin/gbrowse_metadb_config.pl-375- print STDERR "- Data Source not found for $file (owned by $uploadsid), ";
gbrowse-2.56+dfsg/bin/gbrowse_metadb_config.pl:376: $database->do("UPDATE uploads SET data_source = ? WHERE path = ? AND userid = ?", undef, $data_source, $file, $uploadsid) or print STDERR "could not add to database.\n" . DBI->errstr;
gbrowse-2.56+dfsg/bin/gbrowse_metadb_config.pl-377- print STDERR "added to database.\n" unless DBI->errstr;
##############################################
gbrowse-2.56+dfsg/bin/gbrowse_metadb_config.pl-692- warn "backing up existing users database to $dest";
gbrowse-2.56+dfsg/bin/gbrowse_metadb_config.pl:693: system ('cp',$src,$dest);
gbrowse-2.56+dfsg/bin/gbrowse_metadb_config.pl-694- } elsif ($type =~ /mysql/i) {
##############################################
gbrowse-2.56+dfsg/bin/gbrowse_metadb_config.pl-707- open STDOUT,">$dest" or die "$dest: $!";
gbrowse-2.56+dfsg/bin/gbrowse_metadb_config.pl:708: system('mysqldump',"--user=$db_user","--password=$db_pass",$src);
gbrowse-2.56+dfsg/bin/gbrowse_metadb_config.pl-709- open STDOUT,">&SAVEOUT";
##############################################
gbrowse-2.56+dfsg/bin/gtf2gff3.pl-49-if ($help) {
gbrowse-2.56+dfsg/bin/gtf2gff3.pl:50: print `perldoc $0`;
gbrowse-2.56+dfsg/bin/gtf2gff3.pl-51- exit;
##############################################
gbrowse-2.56+dfsg/bin/gbrowse_grow_cloud_vol.pl-98-print STDERR "Creating lvm physical device.\n";
gbrowse-2.56+dfsg/bin/gbrowse_grow_cloud_vol.pl:99:system("sudo pvcreate $local_device") == 0 or die "pvcreate failed";
gbrowse-2.56+dfsg/bin/gbrowse_grow_cloud_vol.pl-100-
gbrowse-2.56+dfsg/bin/gbrowse_grow_cloud_vol.pl-101-print STDERR "Extending 'volumes' volume group.\n";
gbrowse-2.56+dfsg/bin/gbrowse_grow_cloud_vol.pl:102:system("sudo vgextend volumes $local_device") == 0 or die "vgextend failed";
gbrowse-2.56+dfsg/bin/gbrowse_grow_cloud_vol.pl-103-
##############################################
gbrowse-2.56+dfsg/bin/gbrowse_grow_cloud_vol.pl-108-print STDERR "Extending 'gbrowse' logical volume.\n";
gbrowse-2.56+dfsg/bin/gbrowse_grow_cloud_vol.pl:109:system("sudo lvextend -l +$free /dev/volumes/gbrowse") == 0 or die "lvextend failed";
gbrowse-2.56+dfsg/bin/gbrowse_grow_cloud_vol.pl-110-
##############################################
gbrowse-2.56+dfsg/conf/MobyServices/GbrowseServices.PMS-504-chmod 0755, $file or die "Can't reset permissions for $file: $!\n";
gbrowse-2.56+dfsg/conf/MobyServices/GbrowseServices.PMS:505:exec("$Config{'eunicefix'} $file") if $Config{'eunicefix'} ne ':';
##############################################
gbrowse-2.56+dfsg/conf/plugins/Blat.pm-125-
gbrowse-2.56+dfsg/conf/plugins/Blat.pm:126: my $error = `$blat_executable $host $port $twobit_dir -minIdentity=$minIdentity -nohead -q=$q $in_file $out_file 2>&1 > /dev/null`;
gbrowse-2.56+dfsg/conf/plugins/Blat.pm-127- die "$error" if $error;
##############################################
gbrowse-2.56+dfsg/conf/plugins/CreateBlastDB.pm-111- print "<h3>Executing $formatdb -t 'Bio::DB::GFF Blast Database' -i $outdir/$dbname -p F -o T -a F</h3>";
gbrowse-2.56+dfsg/conf/plugins/CreateBlastDB.pm:112: my $res = system ("$formatdb -t 'Bio::DB::GFF Blast Database' -i $outdir/$dbname -p F -o T -a F");
gbrowse-2.56+dfsg/conf/plugins/CreateBlastDB.pm-113- unless ($res == -1){
##############################################
gbrowse-2.56+dfsg/conf/plugins/PrimerDesigner.pm-665-#} else {
gbrowse-2.56+dfsg/conf/plugins/PrimerDesigner.pm:666: #print Dumper param();
gbrowse-2.56+dfsg/conf/plugins/PrimerDesigner.pm-667-#}
##############################################
gbrowse-2.56+dfsg/docs/pod/CONFIGURE_HOWTO.pod-2474- use Socket;
gbrowse-2.56+dfsg/docs/pod/CONFIGURE_HOWTO.pod:2475: $host = gethostbyaddr(inet_aton($addr),AF_INET);
gbrowse-2.56+dfsg/docs/pod/CONFIGURE_HOWTO.pod-2476-
##############################################
gbrowse-2.56+dfsg/etc/init.d/gbrowse-slave-49- for port in $PORT; do
gbrowse-2.56+dfsg/etc/init.d/gbrowse-slave:50: if [ -e $RUNDIR/$NAME.$port.pid ] && kill -0 `cat $RUNDIR/$NAME.$port.pid` >/dev/null 2>&1 ; then
gbrowse-2.56+dfsg/etc/init.d/gbrowse-slave-51- echo "$NAME already running, use restart instead."
##############################################
gbrowse-2.56+dfsg/etc/init.d/gbrowse-slave-73- if test -e $RUNDIR/$NAME.$port.pid ; then
gbrowse-2.56+dfsg/etc/init.d/gbrowse-slave:74: kill -TERM `cat $RUNDIR/$NAME.$port.pid` >/dev/null 2>&1
gbrowse-2.56+dfsg/etc/init.d/gbrowse-slave-75- killed=1
##############################################
gbrowse-2.56+dfsg/etc/init.d/gbrowse-slave-86- if test -e $RUNDIR/$NAME.$port.pid ; then
gbrowse-2.56+dfsg/etc/init.d/gbrowse-slave:87: kill -0 `cat $RUNDIR/$NAME.$port.pid`
gbrowse-2.56+dfsg/etc/init.d/gbrowse-slave-88- if [ "$?" -eq 0 ]; then
##############################################
gbrowse-2.56+dfsg/etc/init.d/gbrowse-aws-balancer-56- if test -e $PID ; then
gbrowse-2.56+dfsg/etc/init.d/gbrowse-aws-balancer:57: kill -0 `cat $PID`
gbrowse-2.56+dfsg/etc/init.d/gbrowse-aws-balancer-58- if [ "$?" -eq 0 ]; then
##############################################
gbrowse-2.56+dfsg/install_util/gbrowse_ppm_install.pl-67-for my $inst ("cgi_install.pl","htdocs_install.pl","conf_install.pl") {
gbrowse-2.56+dfsg/install_util/gbrowse_ppm_install.pl:68: system("perl","install_util/$inst",@args); #==0
gbrowse-2.56+dfsg/install_util/gbrowse_ppm_install.pl-69- # or die "The install script, $inst, failed. I don't know why\n";;
##############################################
gbrowse-2.56+dfsg/install_util/pod2docs.pl-14- if ('INSTALL.pod' eq basename($File::Find::name)) {
gbrowse-2.56+dfsg/install_util/pod2docs.pl:15: system('pod2text','-l',$File::Find::name,'INSTALL.txt');
gbrowse-2.56+dfsg/install_util/pod2docs.pl-16- } else {
##############################################
gbrowse-2.56+dfsg/install_util/pod2docs.pl-18- if (uc($basename) eq $basename) {
gbrowse-2.56+dfsg/install_util/pod2docs.pl:19: system('pod2text','-l',$File::Find::name,"./docs/$basename");
gbrowse-2.56+dfsg/install_util/pod2docs.pl-20- } else {
gbrowse-2.56+dfsg/install_util/pod2docs.pl:21: system('pod2text','-l',$File::Find::name,"./docs/$basename.txt");
gbrowse-2.56+dfsg/install_util/pod2docs.pl-22- }
##############################################
gbrowse-2.56+dfsg/install_util/GBrowseInstall.pm-1011- or die "Could not find apache executable on this system. Can't figure out version number for config file.";
gbrowse-2.56+dfsg/install_util/GBrowseInstall.pm:1012: my $version = `$apache -v`;
gbrowse-2.56+dfsg/install_util/GBrowseInstall.pm-1013- my ($v) = $version =~ m!Apache/(\S+)!;
##############################################
gbrowse-2.56+dfsg/lib/Bio/DB/Tagger.pm-569- my $oid = $self->object_to_id($objectname,1,$key);
gbrowse-2.56+dfsg/lib/Bio/DB/Tagger.pm:570: $dbh->do("DELETE FROM tag WHERE oid=$oid")
gbrowse-2.56+dfsg/lib/Bio/DB/Tagger.pm-571- if $replace;
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2.pm-511-
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2.pm:512: if ($session->match_nonce($authority,CGI::remote_addr())) {
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2.pm-513- return $session;
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/DataLoader.pm-416- or die DBI->errstr,".\n",$mysql_usage;
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/DataLoader.pm:417: $dbh->do("drop database if exists `$data_path`");
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/DataLoader.pm:418: $dbh->do("create database `$data_path`")
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/DataLoader.pm-419- or die "Could not create $data_path:",DBI->errstr,".\n",$mysql_usage;
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/DataLoader.pm-451- $dsn =~ s/;.+$//;
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/DataLoader.pm:452: $dbh->do("drop database `$dsn`")
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/DataLoader.pm-453- or die "Could not drop $dsn:",DBI->errstr;
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-157- eval {
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm:158: my $ids = $userdb->selectcol_arrayref("SELECT userid FROM users WHERE confirmed=0 AND $days>3");
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-159- for my $id (@$ids) {
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm:160: $userdb->do('DELETE FROM users WHERE userid=?',undef,$id);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm:161: $userdb->do('DELETE FROM session WHERE userid=?',undef,$id);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-162- }
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-316- if ($rows > 0) {
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm:317: $userdb->do('UPDATE users SET gecos=?,email=? WHERE userid=?',undef,$fullname,$email||'',$userid);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-318- } else {
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-397- my $userdb = $self->{dbi};
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm:398: return $userdb->selectrow_array("SELECT username FROM session WHERE userid=?", undef, $userid) || 'an anonymous user';
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-399-}
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-459- my $userid = $self->userid_from_username($username) or return;
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm:460: return $userdb->do('UPDATE users SET confirmed=1 WHERE userid=?',undef,$userid);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-461-}
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-533- eval {
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm:534: $userdb->do('DELETE FROM users WHERE userid=?',undef,$userid);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm:535: $userdb->do('DELETE FROM session WHERE userid=?',undef,$userid);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm:536: $userdb->do('DELETE FROM openid_users WHERE userid=?',undef,$userid);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm:537: $userdb->do('DELETE FROM uploads WHERE userid=?',undef,$userid);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm:538: $userdb->do('DELETE FROM sharing WHERE userid=?',undef,$userid);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-539- $userdb->commit();
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-771- local $userdb->{RaiseError} = 1;
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm:772: $userdb->do("DELETE FROM users WHERE userid=?",undef,$userid);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm:773: $userdb->do("DELETE FROM openid_users WHERE userid=?",undef,$userid);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm:774: $userdb->do("DELETE FROM session WHERE userid=?",undef,$userid);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-775- $userdb->commit();
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-849- if ($column eq 'pass') {
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm:850: my ($pass) = $userdb->selectrow_array('SELECT pass FROM users WHERE userid=?',undef,$userid);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-851- unless ($self->passwd_match($old,$pass)) {
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-943- my $update = $userdb->prepare(
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm:944: "UPDATE users SET pass=? WHERE userid=?") or die $userdb->errstr;
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-945- my $status = $update->execute($secret,$userid) or die $userdb->errstr;
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-993- my $sessionid = $self->get_sessionid($userid);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm:994: $userdb->do('DELETE FROM session where userid=?',undef,$userid);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-995- my $session = $self->globals->session($sessionid);
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-998-
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm:999: $userdb->do('DELETE FROM users WHERE userid=?',undef,$userid);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-1000-
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-1184- # if we get here, we are deleting
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm:1185: my ($correct_pass) = $userdb->selectrow_array('SELECT a.pass FROM users as a WHERE a.userid=?',undef,$users->[0])
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-1186- or return $self->dbi_err;
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-1349- my $userdb = $self->{dbi};
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm:1350: return $userdb->selectrow_array("SELECT remember FROM users WHERE userid = ?", undef, $userid);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-1351-}
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-1357- my $userdb = $self->{dbi};
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm:1358: return $userdb->selectrow_array("SELECT userid FROM openid_users WHERE userid = ?", undef, $userid)? "true" : "false";
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserDB.pm-1359-}
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/DataLoader/sam.pm-58- $self->set_status('recompressing source');
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/DataLoader/sam.pm:59: system ("gzip $source_file");
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/DataLoader/sam.pm-60-}
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-79- # First, check my files.
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm:80: my $uploads = $uploadsdb->selectrow_array("SELECT trackid FROM uploads WHERE path = ? AND userid = ? AND data_source = ?", undef, $filename, $userid, $data_source);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-81- return $uploads if $uploads;
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-83- # Then, check files shared with me.
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm:84: my $shared = $uploadsdb->selectrow_array("SELECT DISTINCT uploads.trackid FROM uploads LEFT JOIN sharing ON uploads.trackid = sharing.trackid WHERE sharing.userid = ? AND uploads.path = ? AND (uploads.sharing_policy = ? OR uploads.sharing_policy = ?) AND data_source = ?", undef, $userid, $filename, "casual", "group", $data_source);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-85- return $shared if $shared;
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-87- # Lastly, check public files.
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm:88: my $public = $uploadsdb->selectrow_array("SELECT trackid FROM uploads WHERE path = ? AND sharing_policy = ? AND data_source = ?", undef, $filename, "public", $data_source);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-89- return $public if $public;
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-111- my $data_source = $self->{data_source};
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm:112: my $rows = $uploadsdb->selectcol_arrayref("SELECT trackid FROM uploads WHERE userid = ? AND sharing_policy <> ? AND imported <> 1 AND data_source=? ORDER BY trackid", undef, $userid, "public", $data_source);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-113- return @$rows;
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-178-;
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm:179: $sql .= "AND u.trackid NOT IN (SELECT trackid FROM sharing WHERE userid=$userid)"
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-180- if $userid;
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-212- my $sql = "SELECT u.trackid FROM uploads u"
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm:213: . " LEFT JOIN (SELECT s.trackid FROM sharing s WHERE s.userid = " . $uploadsdb->quote($userid) . ") s"
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-214- . " USING(trackid) WHERE s.trackid IS NULL"
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-232- my $data_source = $self->{data_source};
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm:233: my $rows = $uploadsdb->selectcol_arrayref("SELECT trackid FROM uploads WHERE sharing_policy <> 'public' AND imported = 1 AND data_source = ? AND userid = ? ORDER BY trackid", undef, $data_source, $userid);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-234- return @$rows;
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-260- my $userid = $self->{userid};
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm:261: $sql .= "AND a.trackid NOT IN (SELECT trackid FROM sharing WHERE userid=$userid)"
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-262- if $userid;
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-288- #Since upload IDs are all the same size, we don't have to worry about one ID repeated inside another so this next line is OK. Still, might be a good idea to secure this somehow?
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm:289: my $rows = $uploadsdb->selectcol_arrayref("SELECT DISTINCT uploads.trackid FROM uploads LEFT JOIN sharing ON uploads.trackid = sharing.trackid WHERE sharing.userid = ? AND sharing.public = 0 AND (uploads.sharing_policy = ? OR uploads.sharing_policy = ?) AND uploads.userid <> ? AND uploads.data_source = ? ORDER BY uploads.trackid", undef, $userid, "group", "casual", $userid, $data_source);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-290- return @$rows;
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-378-
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm:379: return $uploadsdb->do("DELETE FROM sharing WHERE trackid = ? AND userid = ? AND public = ?", undef, $file, $userid, $public_flag);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-380- } else {
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-439- $value =~ s/\s+$//;
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm:440: my $result = $uploadsdb->do("UPDATE uploads SET $field = ? WHERE trackid = ?", undef, $value, $file);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-441- $self->update_modified($file);
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-443- } else {
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm:444: return $uploadsdb->selectrow_array("SELECT $field FROM uploads WHERE trackid = ?", undef, $file);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-445- }
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-454- # Do not swap out this line for a field() call, since it's used inside field().
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm:455: return $uploadsdb->do("UPDATE uploads SET modification_date = $now WHERE trackid = " . $uploadsdb->quote($file));
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-456-}
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-526- my $now = $self->nowfun;
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm:527: my $result = $uploadsdb->do("DELETE FROM uploads WHERE trackid='$fileid'");
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-528- $uploadsdb->do("INSERT INTO uploads (trackid, userid, path, description, imported, creation_date, modification_date, sharing_policy, data_source ) VALUES (?, ?, ?, ?, ?, $now, $now, ?, ?)", undef, $fileid, $userid, $filename, $description, $imported, $shared, $data_source)
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-549- my $uploadsdb = $self->{uploadsdb};
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm:550: $uploadsdb->do("DELETE FROM uploads WHERE trackid = ?", undef, $file);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm:551: $uploadsdb->do("DELETE FROM sharing WHERE trackid = ?", undef, $file);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-552-
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-626- my $uploadsdb = $self->{uploadsdb};
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm:627: my $results = $uploadsdb->selectcol_arrayref("SELECT trackid FROM sharing WHERE trackid = ? AND userid = ?", undef, $file, $userid);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-628- return (@$results > 0);
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-662- my $uploadsdb = $self->{uploadsdb};
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm:663: my $usersref = $uploadsdb->selectcol_arrayref("SELECT userid FROM sharing WHERE trackid = ? AND public = ? ORDER BY userid", undef, $file, $public);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/UserTracks/Database.pm-664- return @$usersref;
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm-161- } else {
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm:162: $host ||= gethostbyaddr(inet_aton($addr),AF_INET);
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm-163- next unless $host;
##############################################
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/Render.pm-477- my $nonce = Bio::Graphics::Browser2::Util->generate_id;
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/Render.pm:478: my $ip = CGI::remote_addr();
gbrowse-2.56+dfsg/lib/Bio/Graphics/Browser2/Render.pm-479-
##############################################
gbrowse-2.56+dfsg/lib/Legacy/Graphics/Browser.pm-3202- } else {
gbrowse-2.56+dfsg/lib/Legacy/Graphics/Browser.pm:3203: $host ||= gethostbyaddr(inet_aton($addr),AF_INET);
gbrowse-2.56+dfsg/lib/Legacy/Graphics/Browser.pm-3204- next unless $host;
##############################################
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/etc/init.d/gbrowse-slave-46- for port in $PORT; do
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/etc/init.d/gbrowse-slave:47: if [ -e $RUNDIR/$NAME.$port.pid ] && kill -0 `cat $RUNDIR/$NAME.$port.pid` >/dev/null 2>&1 ; then
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/etc/init.d/gbrowse-slave-48- echo "$NAME already running, use restart instead."
##############################################
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/etc/init.d/gbrowse-slave-70- if test -e $RUNDIR/$NAME.$port.pid ; then
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/etc/init.d/gbrowse-slave:71: kill -TERM `cat $RUNDIR/$NAME.$port.pid` >/dev/null 2>&1
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/etc/init.d/gbrowse-slave-72- killed=1
##############################################
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/etc/init.d/gbrowse-slave-83- if test -e $RUNDIR/$NAME.$port.pid ; then
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/etc/init.d/gbrowse-slave:84: kill -0 `cat $RUNDIR/$NAME.$port.pid`
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/etc/init.d/gbrowse-slave-85- if [ "$?" -eq 0 ]; then
##############################################
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/bin/gbrowse_metadb_config.pl-306- $settings->{uploadid};
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/bin/gbrowse_metadb_config.pl:307: $database->do("UPDATE session SET uploadsid = ? WHERE sessionid = ?", undef, $uploadsid, $userid) or print STDERR "could not add to database.\n" . DBI->errstr;
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/bin/gbrowse_metadb_config.pl-308- print STDERR "added to database.\n" unless DBI->errstr;
##############################################
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/bin/gbrowse_metadb_config.pl-366- foreach my $file (@files) {
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/bin/gbrowse_metadb_config.pl:367: my @data_source_in_db = $database->selectrow_array("SELECT data_source FROM uploads WHERE path = ? AND userid = ?", undef, $file, $uploadsid);
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/bin/gbrowse_metadb_config.pl-368- unless (@data_source_in_db) {
##############################################
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/bin/gbrowse_metadb_config.pl-370- print STDERR "- Data Source not found for $file (owned by $uploadsid), ";
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/bin/gbrowse_metadb_config.pl:371: $database->do("UPDATE uploads SET data_source = ? WHERE path = ? AND userid = ?", undef, $data_source, $file, $uploadsid) or print STDERR "could not add to database.\n" . DBI->errstr;
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/bin/gbrowse_metadb_config.pl-372- print STDERR "added to database.\n" unless DBI->errstr;
##############################################
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/bin/gbrowse_metadb_config.pl-687- warn "backing up existing users database to $dest";
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/bin/gbrowse_metadb_config.pl:688: system ('cp',$src,$dest);
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/bin/gbrowse_metadb_config.pl-689- } elsif ($type =~ /mysql/i) {
##############################################
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/bin/gbrowse_metadb_config.pl-702- open STDOUT,">$dest" or die "$dest: $!";
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/bin/gbrowse_metadb_config.pl:703: system('mysqldump',"--user=$db_user","--password=$db_pass",$src);
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/bin/gbrowse_metadb_config.pl-704- open STDOUT,">&SAVEOUT";
##############################################
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/install_util/GBrowseInstall.pm-933- or die "Could not find apache executable on this system. Can't figure out version number for config file.";
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/install_util/GBrowseInstall.pm:934: my $version = `$apache -v`;
gbrowse-2.56+dfsg/.pc/debian-packaging-patch/install_util/GBrowseInstall.pm-935- my ($v) = $version =~ m!Apache/(\S+)!;
##############################################
gbrowse-2.56+dfsg/.pc/gbrowse-slave-fix_defaults_path/etc/init.d/gbrowse-slave-46- for port in $PORT; do
gbrowse-2.56+dfsg/.pc/gbrowse-slave-fix_defaults_path/etc/init.d/gbrowse-slave:47: if [ -e $RUNDIR/$NAME.$port.pid ] && kill -0 `cat $RUNDIR/$NAME.$port.pid` >/dev/null 2>&1 ; then
gbrowse-2.56+dfsg/.pc/gbrowse-slave-fix_defaults_path/etc/init.d/gbrowse-slave-48- echo "$NAME already running, use restart instead."
##############################################
gbrowse-2.56+dfsg/.pc/gbrowse-slave-fix_defaults_path/etc/init.d/gbrowse-slave-70- if test -e $RUNDIR/$NAME.$port.pid ; then
gbrowse-2.56+dfsg/.pc/gbrowse-slave-fix_defaults_path/etc/init.d/gbrowse-slave:71: kill -TERM `cat $RUNDIR/$NAME.$port.pid` >/dev/null 2>&1
gbrowse-2.56+dfsg/.pc/gbrowse-slave-fix_defaults_path/etc/init.d/gbrowse-slave-72- killed=1
##############################################
gbrowse-2.56+dfsg/.pc/gbrowse-slave-fix_defaults_path/etc/init.d/gbrowse-slave-83- if test -e $RUNDIR/$NAME.$port.pid ; then
gbrowse-2.56+dfsg/.pc/gbrowse-slave-fix_defaults_path/etc/init.d/gbrowse-slave:84: kill -0 `cat $RUNDIR/$NAME.$port.pid`
gbrowse-2.56+dfsg/.pc/gbrowse-slave-fix_defaults_path/etc/init.d/gbrowse-slave-85- if [ "$?" -eq 0 ]; then
##############################################
gbrowse-2.56+dfsg/.pc/manpages.patch/bin/gtf2gff3.pl-49-if ($help) {
gbrowse-2.56+dfsg/.pc/manpages.patch/bin/gtf2gff3.pl:50: print `perldoc $0`;
gbrowse-2.56+dfsg/.pc/manpages.patch/bin/gtf2gff3.pl-51- exit;
##############################################
gbrowse-2.56+dfsg/.pc/manpages.patch/bin/gbrowse_grow_cloud_vol.pl-98-print STDERR "Creating lvm physical device.\n";
gbrowse-2.56+dfsg/.pc/manpages.patch/bin/gbrowse_grow_cloud_vol.pl:99:system("sudo pvcreate $local_device") == 0 or die "pvcreate failed";
gbrowse-2.56+dfsg/.pc/manpages.patch/bin/gbrowse_grow_cloud_vol.pl-100-
gbrowse-2.56+dfsg/.pc/manpages.patch/bin/gbrowse_grow_cloud_vol.pl-101-print STDERR "Extending 'volumes' volume group.\n";
gbrowse-2.56+dfsg/.pc/manpages.patch/bin/gbrowse_grow_cloud_vol.pl:102:system("sudo vgextend volumes $local_device") == 0 or die "vgextend failed";
gbrowse-2.56+dfsg/.pc/manpages.patch/bin/gbrowse_grow_cloud_vol.pl-103-
##############################################
gbrowse-2.56+dfsg/.pc/manpages.patch/bin/gbrowse_grow_cloud_vol.pl-108-print STDERR "Extending 'gbrowse' logical volume.\n";
gbrowse-2.56+dfsg/.pc/manpages.patch/bin/gbrowse_grow_cloud_vol.pl:109:system("sudo lvextend -l +$free /dev/volumes/gbrowse") == 0 or die "lvextend failed";
gbrowse-2.56+dfsg/.pc/manpages.patch/bin/gbrowse_grow_cloud_vol.pl-110-
##############################################
gbrowse-2.56+dfsg/.pc/manpages.patch/lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm-162- } else {
gbrowse-2.56+dfsg/.pc/manpages.patch/lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm:163: $host ||= gethostbyaddr(inet_aton($addr),AF_INET);
gbrowse-2.56+dfsg/.pc/manpages.patch/lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm-164- next unless $host;
##############################################
gbrowse-2.56+dfsg/.pc/manpages.patch/lib/Bio/Graphics/Browser2/Render.pm-471- my $nonce = Bio::Graphics::Browser2::Util->generate_id;
gbrowse-2.56+dfsg/.pc/manpages.patch/lib/Bio/Graphics/Browser2/Render.pm:472: my $ip = CGI::remote_addr();
gbrowse-2.56+dfsg/.pc/manpages.patch/lib/Bio/Graphics/Browser2/Render.pm-473-
##############################################
gbrowse-2.56+dfsg/.pc/manpages.patch/lib/Legacy/Graphics/Browser.pm-3196- } else {
gbrowse-2.56+dfsg/.pc/manpages.patch/lib/Legacy/Graphics/Browser.pm:3197: $host ||= gethostbyaddr(inet_aton($addr),AF_INET);
gbrowse-2.56+dfsg/.pc/manpages.patch/lib/Legacy/Graphics/Browser.pm-3198- next unless $host;
##############################################
gbrowse-2.56+dfsg/.pc/skip_check_installed_test.patch/install_util/GBrowseInstall.pm-1011- or die "Could not find apache executable on this system. Can't figure out version number for config file.";
gbrowse-2.56+dfsg/.pc/skip_check_installed_test.patch/install_util/GBrowseInstall.pm:1012: my $version = `$apache -v`;
gbrowse-2.56+dfsg/.pc/skip_check_installed_test.patch/install_util/GBrowseInstall.pm-1013- my ($v) = $version =~ m!Apache/(\S+)!;
##############################################
gbrowse-2.56+dfsg/.pc/source_init_functions/etc/init.d/gbrowse-slave-47- for port in $PORT; do
gbrowse-2.56+dfsg/.pc/source_init_functions/etc/init.d/gbrowse-slave:48: if [ -e $RUNDIR/$NAME.$port.pid ] && kill -0 `cat $RUNDIR/$NAME.$port.pid` >/dev/null 2>&1 ; then
gbrowse-2.56+dfsg/.pc/source_init_functions/etc/init.d/gbrowse-slave-49- echo "$NAME already running, use restart instead."
##############################################
gbrowse-2.56+dfsg/.pc/source_init_functions/etc/init.d/gbrowse-slave-71- if test -e $RUNDIR/$NAME.$port.pid ; then
gbrowse-2.56+dfsg/.pc/source_init_functions/etc/init.d/gbrowse-slave:72: kill -TERM `cat $RUNDIR/$NAME.$port.pid` >/dev/null 2>&1
gbrowse-2.56+dfsg/.pc/source_init_functions/etc/init.d/gbrowse-slave-73- killed=1
##############################################
gbrowse-2.56+dfsg/.pc/source_init_functions/etc/init.d/gbrowse-slave-84- if test -e $RUNDIR/$NAME.$port.pid ; then
gbrowse-2.56+dfsg/.pc/source_init_functions/etc/init.d/gbrowse-slave:85: kill -0 `cat $RUNDIR/$NAME.$port.pid`
gbrowse-2.56+dfsg/.pc/source_init_functions/etc/init.d/gbrowse-slave-86- if [ "$?" -eq 0 ]; then
##############################################
gbrowse-2.56+dfsg/.pc/source_init_functions/etc/init.d/gbrowse-aws-balancer-54- if test -e $PID ; then
gbrowse-2.56+dfsg/.pc/source_init_functions/etc/init.d/gbrowse-aws-balancer:55: kill -0 `cat $PID`
gbrowse-2.56+dfsg/.pc/source_init_functions/etc/init.d/gbrowse-aws-balancer-56- if [ "$?" -eq 0 ]; then
##############################################
gbrowse-2.56+dfsg/.pc/init_script_dependency.patch/etc/init.d/gbrowse-aws-balancer-56- if test -e $PID ; then
gbrowse-2.56+dfsg/.pc/init_script_dependency.patch/etc/init.d/gbrowse-aws-balancer:57: kill -0 `cat $PID`
gbrowse-2.56+dfsg/.pc/init_script_dependency.patch/etc/init.d/gbrowse-aws-balancer-58- if [ "$?" -eq 0 ]; then
##############################################
gbrowse-2.56+dfsg/.pc/fix_runlevel.patch/etc/init.d/gbrowse-aws-balancer-56- if test -e $PID ; then
gbrowse-2.56+dfsg/.pc/fix_runlevel.patch/etc/init.d/gbrowse-aws-balancer:57: kill -0 `cat $PID`
gbrowse-2.56+dfsg/.pc/fix_runlevel.patch/etc/init.d/gbrowse-aws-balancer-58- if [ "$?" -eq 0 ]; then
##############################################
gbrowse-2.56+dfsg/.pc/spelling.patch/bin/gtf2gff3.pl-49-if ($help) {
gbrowse-2.56+dfsg/.pc/spelling.patch/bin/gtf2gff3.pl:50: print `perldoc $0`;
gbrowse-2.56+dfsg/.pc/spelling.patch/bin/gtf2gff3.pl-51- exit;
##############################################
gbrowse-2.56+dfsg/.pc/fix_whatis_entry.patch/bin/gbrowse_grow_cloud_vol.pl-98-print STDERR "Creating lvm physical device.\n";
gbrowse-2.56+dfsg/.pc/fix_whatis_entry.patch/bin/gbrowse_grow_cloud_vol.pl:99:system("sudo pvcreate $local_device") == 0 or die "pvcreate failed";
gbrowse-2.56+dfsg/.pc/fix_whatis_entry.patch/bin/gbrowse_grow_cloud_vol.pl-100-
gbrowse-2.56+dfsg/.pc/fix_whatis_entry.patch/bin/gbrowse_grow_cloud_vol.pl-101-print STDERR "Extending 'volumes' volume group.\n";
gbrowse-2.56+dfsg/.pc/fix_whatis_entry.patch/bin/gbrowse_grow_cloud_vol.pl:102:system("sudo vgextend volumes $local_device") == 0 or die "vgextend failed";
gbrowse-2.56+dfsg/.pc/fix_whatis_entry.patch/bin/gbrowse_grow_cloud_vol.pl-103-
##############################################
gbrowse-2.56+dfsg/.pc/fix_whatis_entry.patch/bin/gbrowse_grow_cloud_vol.pl-108-print STDERR "Extending 'gbrowse' logical volume.\n";
gbrowse-2.56+dfsg/.pc/fix_whatis_entry.patch/bin/gbrowse_grow_cloud_vol.pl:109:system("sudo lvextend -l +$free /dev/volumes/gbrowse") == 0 or die "lvextend failed";
gbrowse-2.56+dfsg/.pc/fix_whatis_entry.patch/bin/gbrowse_grow_cloud_vol.pl-110-