===========================================================
.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
t-coffee-13.41.0.28bdc39+dfsg/example/mocca-12-$lib_name="$name.mocca_lib";
t-coffee-13.41.0.28bdc39+dfsg/example/mocca:13:$type=`t_coffee $seq_file -get_type -quiet`;
t-coffee-13.41.0.28bdc39+dfsg/example/mocca-14-chop ($type);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/mocca-30-
t-coffee-13.41.0.28bdc39+dfsg/example/mocca:31:system ($command);
t-coffee-13.41.0.28bdc39+dfsg/example/mocca-32-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/nature_protocol.pl-31- elsif (&pg_is_installed ("curl")){$pg="curl"; $flag="-o";$arg=$curl_arg;}
t-coffee-13.41.0.28bdc39+dfsg/example/nature_protocol.pl:32: return system ("$pg $address $flag $out>/dev/null 2>/dev/null");
t-coffee-13.41.0.28bdc39+dfsg/example/nature_protocol.pl-33-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/nature_protocol.pl-44- {
t-coffee-13.41.0.28bdc39+dfsg/example/nature_protocol.pl:45: if (system ("perl -M$p -e 1")==$EXIT_SUCCESS){return 1;}
t-coffee-13.41.0.28bdc39+dfsg/example/nature_protocol.pl-46- else {return 0;}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/nature_protocol.pl-49- {
t-coffee-13.41.0.28bdc39+dfsg/example/nature_protocol.pl:50: $r=`which $p 2>/dev/null`;
t-coffee-13.41.0.28bdc39+dfsg/example/nature_protocol.pl-51- if ($r eq ""){return 0;}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/nature_protocol.pl-97-
t-coffee-13.41.0.28bdc39+dfsg/example/nature_protocol.pl:98: if (&pg_is_installed ("wget")){`wget www.google.com -O$tmp >/dev/null 2>/dev/null`;}
t-coffee-13.41.0.28bdc39+dfsg/example/nature_protocol.pl:99: elsif (&pg_is_installed ("curl")){`curl www.google.com -o$tmp >/dev/null 2>/dev/null`;}
t-coffee-13.41.0.28bdc39+dfsg/example/nature_protocol.pl-100-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1056- &url2file("ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_entry_type.txt", $new_file);
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:1057: if ( !-z $new_file){system ("mv $new_file $cache_file"); unlink ($new_file); $new_file=$cache_file;}
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1058- else {unlink($new_file);}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1119- &url2file("http://www.rcsb.org/pdb/rest/getUnreleased",$new_file);
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:1120: if ( !-z $new_file){system ("mv $new_file $cache_file"); unlink ($new_file); $new_file=$cache_file;}
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1121- else {unlink($new_file);}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1176- $pdb=substr ($in,0, 4);
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:1177: chomp(($value1=`grep -c $pdb $ref_file`));
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1178- $pdb=lc($pdb);
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:1179: chomp(($value2=`grep -c $pdb $ref_file`));
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1180- $value=($value1 || $value2)?1:0;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1206-
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:1207: chomp(($value=`grep $pdb $ref_file`));
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1208-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1239- $pdb=substr ($in,0, 4);
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:1240: chomp(($value1=`grep -c $pdb $ref_file`));
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1241- $pdb=lc($pdb);
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:1242: chomp(($value2=`grep -c $pdb $ref_file`));
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1243- $value=($value1 || $value2)?1:0;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1559- $tmp_pdb_file=vtmpnam();
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:1560: `cp $local_pdb_file $tmp_pdb_file`;
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1561- return $tmp_pdb_file;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1579- $tmp_pdb_file=vtmpnam();
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:1580: `cp $local_pdb_file $tmp_pdb_file`;
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1581- return $tmp_pdb_file;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1590- $tmp_pdb_file=vtmpnam();
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:1591: `cp $local_pdb_file $tmp_pdb_file`;
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1592- return $tmp_pdb_file;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1601- $tmp_pdb_file=vtmpnam();
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:1602: `cp $local_pdb_file $tmp_pdb_file`;
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1603- return $tmp_pdb_file;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1617- $tmp_pdb_file=vtmpnam();
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:1618: `cp $local_pdb_file $tmp_pdb_file`;
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1619- return $tmp_pdb_file;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1643- &debug_print ("\n\tFile Found Remotely");
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:1644: if (($r=safe_system ( "$netcompression_pg $compressed_tmp_file_name")!=$EXIT_SUCCESS) && $attempts<5)
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1645- {
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1671- {
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:1672: `cp $return_value $cache/$pdb_file.pdb`;
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:1673: #`t_coffee -other_pg clean_cache.pl -file $pdb_file.pdb -dir $cache`;
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1674- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1691- $file=~s/\/\//\//g;
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:1692: if (-B $file && ($file=~/\.Z/)) {`cp $file $tmp.Z`;`rm $tmp`;`gunzip $tmp.Z $SILENT`;$r=$tmp;}
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:1693: elsif (-B $file && ($file=~/\.gz/)){`cp $file $tmp.gz`;`gunzip $tmp.gz $SILENT`;return $r=$tmp;}
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:1694: elsif (-B $file ){`cp $file $tmp.gz`;`gunzip $tmp.gz $SILENT`;$r=$tmp;}
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1695- elsif ( -e $file ) {$r= $file;}
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:1696: elsif ( -e "$file.gz" ){ `cp $file.gz $tmp.gz`;`gunzip $tmp.gz $SILENT`;$r=$tmp;}
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:1697: elsif ( -e "$file.Z") {`cp $file.Z $tmp.Z`; `gunzip $tmp.Z $SILENT`;$r=$tmp;}
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1698- else {$r= $file;}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1775- elsif (&pg_is_installed ("curl")){$pg="curl"; $flag="-o";$arg=$curl_arg;}
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:1776: return safe_system ("$pg $flag$out $address >/dev/null 2>/dev/null");
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-1777-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-5520- close ($g);
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:5521: safe_system ("mv $fname $fname.old");
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-5522- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-5655- {
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:5656: `rm -rf $dir`;
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-5657- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-5728- set_lock($$, " -SHELL- $com (tcg)");
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:5729: exec ($com);
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-5730- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-5747- lock4tc ($pid, "LRELEASE", "LERROR", "");
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:5748: return safe_system ($com, $ntry, ++$ctry);
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-5749- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-5816- {
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:5817: if (safe_system ("perl -M$p -e 1")==$EXIT_SUCCESS){return 1;}
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-5818- else {return 0;}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-5821- {
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:5822: $r=`which $p 2>/dev/null`;
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-5823- if ($r eq ""){return 0;}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-5837-
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:5838: if (&pg_is_installed ("wget")){`wget www.google.com -O$tmp >/dev/null 2>/dev/null`;}
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:5839: elsif (&pg_is_installed ("curl")){`curl www.google.com -o$tmp >/dev/null 2>/dev/null`;}
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-5840-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-5896- $pdb=substr ($in,0, 4);
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:5897: chomp(($value1=`grep -c $pdb $ref_file`));
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-5898- $pdb=lc($pdb);
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb:5899: chomp(($value2=`grep -c $pdb $ref_file`));
t-coffee-13.41.0.28bdc39+dfsg/example/extract_from_pdb-5900- $value=($value1 || $value2)?1:0;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2consan_aln.pl-120- $cmd = "sed -e '1d' $frawout";
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2consan_aln.pl:121: system("$cmd > $fstk");
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2consan_aln.pl-122- if ($? != 0) {
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2consan_aln.pl-171- #
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2consan_aln.pl:172: system("/usr/bin/time -p -o $ftimelog $cmd >$frawout 2>$ferrlog");
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2consan_aln.pl-173- if ($? != 0) {
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-171- $seq=&vtmpnam();
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:172: `t_coffee -other_pg seq_reformat -in $cdna_seq -action +clean_cdna >$clean_cdna_seq`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:173: `t_coffee -other_pg seq_reformat -in $clean_cdna_seq -action +translate >$seq`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-174-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-181- if ( $alignpg eq "t_coffee")
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:182: {`$alignpg $seq -outfile=$msa >/dev/null 2>/dev/null`;}
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-183- elsif ( $alignpg eq "muscle")
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-184- {
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:185: `$alignpg -in $seq > $msa 2>/dev/null`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-186- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-188- {
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:189: `$alignpg -infile=$seq -outfile=$msa -quicktree >/dev/null 2>/dev/null`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-190- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-192- {
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:193: `$alignpg $seq > $msa >/dev/null 2>/dev/null`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-194- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-196- {
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:197: `$alignpg -in=$seq -outfile=$msa`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-198- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-207- $msa2="$suffix.cdna_msa";
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:208: `t_coffee -other_pg seq_reformat -in $clean_cdna_seq -in2 $msa -action +thread_dna_on_prot_aln -output fasta_aln >$msa2`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-209- $msa=$msa2;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-226- $lmsa= &vtmpnam ();
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:227: `t_coffee -other_pg seq_reformat -in $msa -output phylip_aln > $lmsa`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-228-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-237- close (F);
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:238: `seqboot$exec_extension < $seqboot_c`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-239- if ( -e "outfile"){ print "[OK]\n";}
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-240- else { print "[FAILED]\n";&my_exit (EXIT_FAILURE);}
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:241: `mv outfile $seqboot_o`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-242- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-244- {
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:245: `cp $lmsa $seqboot_o`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-246- }
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-247-
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:248: if ($rmsa){`cp $seqboot_o $rmsa`;}
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-249-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-268- close (F);
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:269: `protdist$exec_extension < $protdist_c`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-270- if ( -e "outfile"){ print "[OK]\n";}
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-271- else { print "[FAILED]\n";&my_exit (EXIT_FAILURE);}
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:272: `mv outfile $protdist_o`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-273-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-281- close (F);
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:282: `protdist$exec_extension < $protdist_c`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-283- if ( -e "outfile"){ print "[OK]\n";}
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-284- else { print "[FAILED]\n";&my_exit (EXIT_FAILURE);}
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:285: `mv outfile $protdist_o`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-286- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-292- print "MSA: $msa\n";
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:293: `cp $msa $protdist_o`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-294- $n=1;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-325-
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:326: `neighbor$exec_extension < $nb_c`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-327- if ( -e "outtree"){ print "[Neighbor OK]\n";}
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-328- else { print "[FAILED]\n";&my_exit (EXIT_FAILURE);}
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:329: `mv outtree $nb_o`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-330- unlink ("outfile");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-343- close (F);
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:344: `protpars$exec_extension < $nb_c`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-345- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-352- close (F);
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:353: `dnapars$exec_extension < $nb_c`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-354- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-356- else { print "[FAILED]\n";&my_exit (EXIT_FAILURE);}
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:357: `mv outtree $nb_o`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-358- unlink ("outfile");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-376- close (F);
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:377: `dnaml$exec_extension < $nb_c`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-378- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-380- else { print "[FAILED]\n";&my_exit (EXIT_FAILURE);}
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:381: `mv outtree $nb_o`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-382- unlink ("outfile");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-387- {
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:388: `cp $msa $nb_o`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-389- $n=2;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-391-
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:392:if ($rmsa && -e $seqboot_o){print "\nOutput List of $n Replicate MSA: $rmsa\n";`cp $seqboot_o $rmsa`;}
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:393:if ($rmat && -e $protdist_o){print "\nOutput List of $n Replicate MATRICES: $rmat\n";`cp $protdist_o $rmat`;}
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:394:if ($rtree && -e $nb_o){print "\nOutput List of $n Replicate TREES: $rtree\n";`cp $nb_o $rtree`;}
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-395-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-405- close (F);
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:406: `consense$exec_extension < $con_c`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-407- if ( -s "outtree" > 0) { print "[OK]\n";}
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-408- else { print "[FAILED]\n";&my_exit (EXIT_FAILURE);}
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:409: `mv outtree $con_o`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-410- unlink ("outfile");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-413- {
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:414: `cp $nb_o $con_o`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-415- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-417-
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:418:`cp $con_o $out`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-419-if ( !-e $out)
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-426- print "\nOutput Bootstrapped Tree: $out\n";
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl:427: $avg=`t_coffee -other_pg seq_reformat -in $out -action +avg_bootstrap`;
t-coffee-13.41.0.28bdc39+dfsg/example/msa2bootstrap.pl-428- $avg=~s/\n//g;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa-112- print STDERR "\n Step $step: Gather all the sequences into the tmp file: [$seq]";$step++;
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa:113: &my_system ("t_coffee $in_seq -convert -quiet -output fasta_seq -outfile=$seq -maxnseq 0");
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa-114- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa-189-
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa:190: &my_system ("t_coffee -special_mode quickaln -in $seq -outfile $aln -quiet");
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa:191: &my_system ("$seq_reformat -in $aln -action +aln2tree +tree2dpatree -output newick >$newtree");
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa-192- return $newtree;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa-199-
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa:200: &my_system("$seq_reformat -in $aln -action +seq2dpatree -output newick > $newtree");
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa-201- return $newtree;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa-207-
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa:208: &my_system("$seq_reformat -in $aln -action +aln2tree +tree2dpatree -output newick > $newtree");
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa-209- return $newtree;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa-257- #1 extract the groups
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa:258: &my_system ("$seq_reformat -in $tree -action +tree2group $N $ID $prefix > $group_file");
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa-259- $n=group_file2ngroups($group_file);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa-313- $gl{'Tree'}=&vtmpnam();
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa:314: &my_system ("$seq_reformat -in $tree -action +collapse_tree $group_file -output newick > $gl{'Tree'}");
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa-315-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa-355- {
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa:356: &my_system ($command);
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa-357- $command="t_coffee -special_mode quick_aln S$f -outfile=$Output -quiet";
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa-378-
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa:379: &my_system ($command);
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa-380- return $outfile;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa-389- if ( $dpa_debug) {print STDERR "\nCOMMAND: $command";}
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa:390: $status=system ($command);
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa-391-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa-420- $list=vtmpnam();
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa:421: `ls -1 | grep $tmp_prefix>$list`;
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa-422-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-167-
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:168:if (-d "mcoffee"){`cp mcoffee/* $TCM`;}
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-169-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-250- {
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:251: `rm $BIN/$pg $BIN/$pg.exe $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-252- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-258- print "------- cleaning executables -----\n";
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:259: `rm bin/* $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-260- exit ($EXIT_SUCCESS);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-345-
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:346:if ($clean==1 && ($BASE=~/install4tcoffee/) ){print "*------ Clean Installation Directory: $BASE\n";`rm -rf $BASE`;}
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-347-foreach my $pg (keys(%PG)){if ($PG{$pg}{install} && $PG{$pg}{status}==0){exit ($EXIT_FAILURE);}}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-492- {
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:493: if ( system ("perl -M$p -e 1")==$EXIT_SUCCESS){$ret=1;}
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-494- else {$ret=0;}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-503- {
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:504: $r=`which $p 2>/dev/null`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-505- if ($r eq ""){$ret=0;}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-519-
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:520: if (-e "$BIN/t_coffee"){`$CP $BIN/t_coffee $INSTALL_DIR`};
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:521: `cp $BIN/* $PLUGINS_DIR`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-522- $copied=1;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-610- {
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:611: if ( $OS eq "windows"){`perl -M$compiler -e 'install $pg'`;}
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:612: elsif ( $ROOT eq "sudo"){system ("sudo perl -M$compiler -e 'install $pg'");}
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:613: else {system ("su root -c perl -M$compiler -e 'install $pg'");}
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-614- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-666- {
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:667: `$CP $DOWNLOAD_DIR/$distrib .`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-668- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-677-
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:678: `mv $wget_tmp $distrib`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:679: `$CP $distrib $DOWNLOAD_DIR/`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-680- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-716- print "\n------- Compiling/Installing $pg\n";
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:717: `make clean $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-718-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-737- #old style distribution
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:738: `rm *.o sap sap.exe ./util/aa/*.o ./util/wt/.o $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-739- &flush_command ("make $arguments sap");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-786- repo_store("fsa", "$BIN/bin");
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:787: `mv $BIN/bin/* $BIN`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:788: `rmdir $BIN/bin`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-789- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-796- &flush_command("make $arguments clustalw");
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:797: `$CP $pg $BIN $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-798- repo_store($pg);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-812- chdir "$base/core";
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:813: `make clean $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-814- &flush_command ("make $arguments");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-818- chdir "$base/extensions";
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:819: `make clean $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-820- &flush_command ("make $arguments");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-830- {
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:831: `$CP mafft/lib/* $BIN`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:832: `$CP mafft/bin/mafft $BIN`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-833- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-835- `gzip mafft.tar`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:836: `mv mafft.tar.gz $BIN`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-837-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-895-
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:896: `rm *.exe $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-897- &flush_command ("make $arguments probcons");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-908- &add_C_libraries("./Main.cc", "iomanip", "cstring","climits");
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:909: `rm *.exe $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-910- &flush_command ("make $arguments probcons");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-919- {
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:920: `rm *.o muscle muscle.exe $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-921- if ($OS eq "macosx" || $OS eq "linux")
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-940- {
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:941: `rm *.o muscle muscle.exe $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-942- &flush_command ("./mk");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-977- &add_C_libraries("./Amap.cc", "iomanip", "cstring","climits");
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:978: `make clean $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-979- &flush_command ("make $arguments all");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1077- print "\n------- Compiling TMalign\n";
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:1078: `rm TMalign TMalign.exe $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1079- if ( $FC ne ""){&flush_command ("make -i $PG{Fortran}{arguments} TMalign");}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1130- {
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:1131: `rm x $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1132- if ( url2file("$download","x")==$EXIT_SUCCESS)
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1133- {
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:1134: `mv x $name`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1135- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1147- {
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:1148: `gunzip $name`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:1149: `tar -xvf $pg.tar`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1150- chdir $pg;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1158- {
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:1159: `$CP $TMP/$pg/bin/* $BIN $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:1160: `$CP $TMP/$pg/lib/* $BIN $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1161- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1164- {
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:1165: if (-e "$TMP/$pg/data"){`$CP $TMP/$pg/data/* $TCM $SILENT`;}
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:1166: if (!($pg=~/\*/)){`rm -rf $pg`;}
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1167- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1171- &check_cp ("$pg", "$BIN");
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:1172: `chmod u+x $BIN/$pg`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1173- unlink ($pg);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1211-
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:1212: `$CP $from $to`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1213- return 1;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1222- # extract the package name from the specified path
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:1223: my $pg =`basename $_[0]`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1224- chomp($pg);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1231- # clean the cache path if exists and create it again
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:1232: `rm -rf $CACHE`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:1233: `mkdir -p $CACHE`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1234-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1238- if( -f $path ) {
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:1239: `cp $path $CACHE`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1240- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1248- if( $_file ne "." && $_file ne "..") {
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:1249: `cp $path/$_file $CACHE`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1250- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1272- print "-------- Module \"$pg\" found on repository cache. Using copy on path: $CACHE\n";
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:1273: `cp $CACHE/* $BIN`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1274- return 1;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1291- my @fl;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:1292: chomp(@fl=`ls -1 $f`);
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1293- return @fl;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1364-
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:1365: if ( system ($cmd)==$EXIT_SUCCESS){return $EXIT_SUCCESS;}
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1366- else
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1368- print "------- $txt\n";
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:1369: if ( $ROOT eq "sudo"){return system ("sudo $cmd");}
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:1370: else {return system ("su root -c \"$cmd\"");}
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1371- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1435- ($address, $name)=($download=~/(.*)\/([^\/]+)$/);
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:1436: `rm x $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1437- if (&url2file ($file,"x")==$EXIT_SUCCESS)
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1439- print "------- Susscessful upload of $name";
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:1440: `mv x $name`;
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1441- $file=$name;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1908-
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:1909: system ("mv $file $file.old");
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1910- open ($O, ">$file");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1933-
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl:1934: system ("mv $file $file.old");
t-coffee-13.41.0.28bdc39+dfsg/example/install.pl-1935- open ($O, ">$file");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/RNAplfold2tclib.pl-116- $cmd = "RNAplfold -W $window_size < $fnametmp >/dev/null";
t-coffee-13.41.0.28bdc39+dfsg/example/RNAplfold2tclib.pl:117: system($cmd);
t-coffee-13.41.0.28bdc39+dfsg/example/RNAplfold2tclib.pl-118-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/RNAplfold2tclib.pl-166- #$cmd = "gzip -qf $fps";
t-coffee-13.41.0.28bdc39+dfsg/example/RNAplfold2tclib.pl:167: #system($cmd);
t-coffee-13.41.0.28bdc39+dfsg/example/RNAplfold2tclib.pl-168- #if ($? != 0) {
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl-92-if ($cov) {$cov_action= " +sim_filter _aln_c$cov ";}
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl:93:&safe_system("t_coffee -other_pg seq_reformat -in $fmsq1 -action +convert 'BOUJXZ-' $cov_action $trim_action -output fasta_aln -out $fmsq2");
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl-94-my (%pred, %seq, %predA);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl-172- output_fasta_seq (\%seq,$tmp_in, "seq");
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl:173: `hmmtop -pi=mpred -if=$tmp_in -sf=FAS -pl 2>/dev/null >$tmp_out`;
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl-174- open ($o, ">$outfile");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl-200-
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl:201: `hmmtop -if=$tmp_in -sf=FAS -pl 2>/dev/null >$tmp_out`;
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl-202-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl-238- output_fasta_seq (\%seq,$tmp_in, "seq");
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl:239: `gorIV -prd $tmp_in -seq $GOR_SEQ -obs $GOR_OBS >$tmp_out`;
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl-240- open ($o, ">$tmp");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl-403-
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl:404: safe_system ( "t_coffee -other_pg seq_reformat -in $aln -struc_in $struc -struc_in_f number_fasta -output color_html -out $out");
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl-405- return;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl-602- close ($g);
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl:603: safe_system ("mv $fname $fname.old");
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl-604- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl-737- {
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl:738: `rm -rf $dir`;
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl-739- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl-810- set_lock($$, " -SHELL- $com (tcg)");
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl:811: exec ($com);
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl-812- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl-829- lock4tc ($pid, "LRELEASE", "LERROR", "");
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl:830: return safe_system ($com, $ntry, ++$ctry);
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl-831- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl-898- {
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl:899: if (safe_system ("perl -M$p -e 1")==$EXIT_SUCCESS){return 1;}
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl-900- else {return 0;}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl-903- {
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl:904: $r=`which $p 2>/dev/null`;
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl-905- if ($r eq ""){return 0;}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl-919-
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl:920: if (&pg_is_installed ("wget")){`wget www.google.com -O$tmp >/dev/null 2>/dev/null`;}
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl:921: elsif (&pg_is_installed ("curl")){`curl www.google.com -o$tmp >/dev/null 2>/dev/null`;}
t-coffee-13.41.0.28bdc39+dfsg/example/fasta_seq2hmmtop_fasta.pl-922-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/clean_cache.pl-151- print F "$tot_size";
t-coffee-13.41.0.28bdc39+dfsg/example/clean_cache.pl:152: if ( -e $new_name_file){`mv $new_name_file $name_file`;}
t-coffee-13.41.0.28bdc39+dfsg/example/clean_cache.pl-153- close (F);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2-22-$seq=vtmpnam();
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2:23:`t_coffee $in_seq -convert -output fasta_seq -outfile=$seq`;
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2-24-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2-38- $ref_aln=vtmpnam();
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2:39: `t_coffee -seq=$seq -very_fast -outfile=$ref_aln -quiet`;
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2-40-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2-45- $sim_mat=vtmpnam();
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2:46: `seq_reformat -in $ref_aln -output sim > $sim_mat`;
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2-47- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2-51- $core_seq=vtmpnam();
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2:52: `seq_reformat -in $ref_aln -action +trimTC N$max_nseq -output fasta_seq > $core_seq`;
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2-53- }
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2:54:@core_name=`seq_reformat -in $core_seq -output name `;
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2-55-
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2:56:@tot_name=`seq_reformat -in $seq -output name `;
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2-57-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2-115-
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2:116: `seq_reformat -in $seq -action +lower +keep_name +extract_seq @g_list -output fasta_seq > $g_seq`;
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2-117-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2-126- print STDERR "[t_coffee]\n";
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2:127: `t_coffee $g_seq -outfile=$g_aln -quiet $arg_list`;
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2-128- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2-131- print STDERR "[t_coffee_dpa]\n";
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2:132: `t_coffee_dpa2 $g_seq -outfile=$g_aln $arg_list -sim_matrix $sim_matrix -dpa_nseq $dpa_nseq`;
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2-133- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2-143-
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2:144: `t_coffee -profile @profile_list $arg_list -outfile=$prf -quiet`;
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2-145- $n=$seq_list{"unused"}{'nseq'};
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2-152-
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2:153: `seq_reformat -in $seq -action +lower +keep_name +extract_seq $s -output fasta_seq > $new_seq`;
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2:154: `t_coffee -profile $prf $new_seq $arg_list -outfile=$new_prf`;
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2:155: `cp $new_prf $prf`;
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2-156- }
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2-157- $s=$seq_list{"unused"}{$a};
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2:158: `seq_reformat -in $seq -action +lower +keep_name +extract_seq $s -output fasta_seq > $new_seq`;
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2-159- @profile_list=($prf, $new_seq);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2-170-
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2:171:`t_coffee -profile @profile_list $arg_list`;
t-coffee-13.41.0.28bdc39+dfsg/example/t_coffee_dpa2-172-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-260- {
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:261: &safe_system ("t_coffee -other_pg fasta_seq2hmmtop_fasta.pl -in=seqfile -out=$lib_name -arch=$arch -psv=$psv");
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-262- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-492-
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:493: safe_system ("$hh -name=$s{$seq}{name} -method=search -db=$db -seq=seqfile -outfile=$profile_name");
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-494- if (-e $profile_name){$nseq=fasta2nseq($profile_name);}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-641-
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:642: my $value= &safe_system ("t_coffee -other_pg extract_from_pdb -model_type $pdb > $f");
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-643- my $r=&file2string ($f);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-653-
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:654: my $value= &safe_system ("t_coffee -other_pg extract_from_pdb -model_type $pdb > $f");
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-655- my $r=&file2string ($f);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-668-
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:669: $value= &safe_system ("t_coffee -other_pg extract_from_pdb -is_released_pdb_name $pdb > $f");
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-670- my $r=&file2string ($f);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-689-
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:690: #&safe_system ("formatdb -i $db");
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:691: if ($blast eq "blastp"){&safe_system ("blastp -db $db -query $infile -out io -outfmt 5 -seg yes");}
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:692: elsif ($blast eq "blastn"){&safe_system ("blastn -query $infile -db $db -outfmt 5 -word_size 4 -out io");}
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-693-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-759- }
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:760: &safe_system ("formatdb -i $infile");
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:761: &safe_system ("blastall -i $infile -d $infile -m7 -o io");
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-762- &set_blast_type ("io");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-833- {
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:834: `muscle -in seq.pep -out result.aln $param`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-835- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-845- {
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:846: `$method -d=seq.pep -o=result.aln -quiet 2>/dev/null`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-847- `mv result.aln.1.fas result.aln`;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-854- {
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:855: `$method -infile=seq.pep -outfile=result.aln`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-856- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-887- {
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:888: &safe_system ("$method -infile=seq.pep -pdbfile1=struc.pdb -outfile=result.aln $param>x 2>x");
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-889- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-914- $command="t_coffee -other_pg dalilite.pl --pdb1 $id1 --chainid1 $c1 --pdb2 $id2 --chainid2 $c2 --email=$EMAIL >dali_stderr 2>dali_stderr";
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:915: $dali=`$command`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-916-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-980- {
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:981: if ( &safe_system ("DaliLite -pairwise pdb1.pdb pdb2.pdb >tmp1")==$EXIT_SUCCESS)
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-982- {
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1016- {
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1017: if ( &safe_system ("TMalign pdb1.pdb pdb2.pdb >tmp1")==$EXIT_SUCCESS)
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1018- {
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1040- {
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1041: if ( &safe_system ("mustang -i pdb1.pdb pdb2.pdb -F fasta >/dev/null 2>/dev/null")==$EXIT_SUCCESS)
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1042- {
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1052- {
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1053: if ( &safe_system ("$method -pdbfile1=pdb1.pep -pdbfile2=pdb2.pdb -outfile=result.aln $param>x 2>x")==$EXIT_SUCCESS)
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1054- {
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1109-
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1110: safe_system("runsara.py $pdbfile1 $chain1 $pdbfile2 $chain2 -s -o $tmp_file --limitation 5000 > /dev/null 2> /dev/null");
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1111- if ($ENV{X3DNA_4_SARA}){$ENV{PATH}=$path;}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1149- {
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1150: `clustalw -profile1=$profile1 -profile2=$profile2 -outfile=$outfile`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1151- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1154-
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1155: `clustalo --p1 $profile1 --p2 $profile2 -o $outfile --force`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1156- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1162- {
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1163: `$method -profile1=$profile1 -profile2=$profile2 -outfile=$outfile $param> /dev/null 2>/dev/null`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1164- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1176- {
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1177: if (safe_system ("perl -M$p -e 1")==$EXIT_SUCCESS){return 1;}
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1178- else {return 0;}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1181- {
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1182: $r=`which $p 2>/dev/null`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1183- if ($r eq ""){$r=0;}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1209-
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1210: if (&pg_is_installed ("wget")){`wget www.google.com -O$tmp >/dev/null 2>/dev/null`;}
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1211: elsif (&pg_is_installed ("curl")){`curl www.google.com -o$tmp >/dev/null 2>/dev/null`;}
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1212-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1254- push (@TMPDIR_LIST, $tmp_dir);
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1255: `mkdir $tmp_dir`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1256- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1259- {
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1260: if (-e $list[$a]){ `cp $list[$a] $tmp_dir/$list[$a+1]`;}
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1261- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1276- chdir $initial_dir;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1277: # `t_coffee -other_pg seq_reformat -in $tmp_dir/$list[0] -output fasta_aln -out $tmp_dir/result2.aln`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1278: `cp $tmp_dir/$list[0] $tmp_dir/result2.aln`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1279- if ( $list[1] eq "stdout")
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1285- {
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1286: `mv $tmp_dir/result2.aln $list[1]`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1287- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1290- {
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1291: if (-e ("$tmp_dir/$f")){`mv $tmp_dir/$f .`;}
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1292- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1367-
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1368: safe_system ("$hh -method=align -profile1=$aln1 -profile2=$aln2 -outfile=$outfile");
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1369- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1400- $command="hhalign -i $h{0}{a3m} -t $h{1}{a3m} -tc $outfile.tmp -rank 1 -mapt 0 $param";
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1401: `$command`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1402-
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1403: # `hhalign -i $h{0}{a3m} -t $h{1}{a3m} -tc $outfile.tmp -rank 1 -mapt 0 -gapf 0.8 -gapg 0.8`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1404-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1436-
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1437: `cp $aln $$.hhh_aln`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1438- $command="t_coffee -other_pg seq_reformat -in $aln -output hasch";
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1439: $hv=`$command`;chomp ($hv);
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1440-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1446- $x=`which hhconsensus`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1447: `hhconsensus -M 50 -i $h{aln} -oa2m $h{a2m}`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1448- if (!-e $h{a2m})
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1453-
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1454: `hhconsensus -M 50 -i $h{aln} -oa3m $h{a3m}`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1455- if (!-e $h{a3m})
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1459- }
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1460: `buildali.pl $h{a3m} -n 1`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1461- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1463-
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1464: $h{a2m_seq}=`head -n 2 $h{a2m} | grep -v ">"`;chomp ($h{a2m_seq});
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1465: $h{a3m_seq}=`head -n 2 $h{a3m} | grep -v ">"`;chomp ($h{a3m_seq});
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1466- $h{cons}=$h{a2m_seq};
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1467: $h{seq}=`head -n 2 $h{aln} | grep -v ">"`;chomp ($h{seq});
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1468-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1485-
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1486: $name=`head -n 2 $h{aln} | grep ">"`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1487- $name=~/\>(\S+)/;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1489-
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1490: `cp $h{a2m} $i.a2m`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1491: `cp $h{a3m} $i.a3m`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:1492: `cp $h{aln} $i.hh_aln`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-1493-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2308- {
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2309: &safe_system ("t_coffee -other_pg seq_reformat -in $tmp -action +trim _aln_n$trim\_K1 -output fasta_aln -out $outfile");
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2310- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2312- {
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2313: &safe_system ("t_coffee -other_pg seq_reformat -in $tmp -action +trim _aln_%%$trim\_K1 -output fasta_aln -out $outfile");
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2314- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2317- {
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2318: &safe_system ("mv $tmp $outfile");
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2319- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2399-
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2400: `gorIV -prd $infile -seq $gor_seq -obs $gor_obs > gor_tmp`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2401- open (GR, ">$outfile");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2451- print "\tPSITM: kept $p{n} Homologues for Sequence $p{0}{name}\n";
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2452: &safe_system ("t_coffee -other_pg fasta_seq2hmmtop_fasta.pl -in=tm_input -out=$outfile -output=cons -cov=70 -trim=95 -arch=$arch -psv=$psv");
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2453- unlink ("tm_input");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2493- print "\tGORTM: kept $p{n} Homologues for Sequence $p{0}{name}\n";
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2494: &safe_system ("t_coffee -other_pg fasta_seq2hmmtop_fasta.pl -in=gor_input -out=$outfile -output=cons -cov=70 -trim=95 -gor_seq=$gor_seq -gor_obs=$gor_obs -mode=gor");
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2495- unlink ("tm_input");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2529- $command="t_coffee -other_pg wublast.pl --email $EMAIL $infile -D $db -p $cl_method --outfile $outfile -o xml>/dev/null 2>$error_log";
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2530: &safe_system ( $command);
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2531: if (-e "$outfile.xml") {`mv $outfile.xml $outfile`;}
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2532- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2537- $command="t_coffee -other_pg blastpgp.pl --email $EMAIL $infile -d $db --outfile $outfile -p $cl_method --mode PSI-Blast>/dev/null 2>$error_log";
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2538: &safe_system ( $command);
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2539-
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2540: if (-e "$outfile.xml") {`mv $outfile.xml $outfile`;}
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2541- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2562- }
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2563: &safe_system ( $command,5);
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2564: if (-e "$outfile.out.xml") {`mv $outfile.out.xml $outfile`;}
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2565: elsif (-e "$outfile.xml.xml"){`mv $outfile.xml.xml $outfile`;}
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2566: elsif (-e "$outfile.out..xml") {`mv $outfile.out..xml $outfile`;}
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2567: elsif (-e "$outfile.xml..xml"){`mv $outfile.xml..xml $outfile`;}
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2568- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2586- $command="$cl_method -db $cl_db -query $infile -out $outfile -outfmt 5 -remote";
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2587: &safe_system ($command);
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2588- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2592- $command="$client -p $method -d $db -i $infile -o $outfile -m 7";
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2593: &safe_system ($command);
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2594- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2601- }
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2602: &safe_system ($command);
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2603- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2629- print "$command\n";
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2630: &safe_system ($command);
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2631- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2677- &cache_file("SET",$infile,$name,$method,$db,$outfile,$SERVER);
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2678: #system ("cp $outfile ~/Dropbox/tmp/cedric.out");
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2679- #die;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2716- {
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2717: `cp $cache_file $outfile`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2718- $CACHE_STATUS="READ CACHE";
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2732- {
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2733: `cp $outfile $cache_file`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2734: if ($cache_file_infile ne ""){ `cp $infile $cache_file_infile`;}
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2735-
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2736- #functions for updating the cache
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2737: #`t_coffee -other_pg clean_cache.pl -file $cache_file_sh -dir $CACHE`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2738: #`t_coffee -other_pg clean_cache.pl -file $cache_file_infile_sh -dir $CACHE`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2739- return 1;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2751- elsif ( !-e $f2){return 0;}
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2752: elsif ($f1 eq "" || $f2 eq "" || `diff $f1 $f2` eq ""){return 1;}
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2753-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2768- {
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2769: return &safe_system ("wget $address -O$out >/dev/null 2>/dev/null");
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2770- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2772- {
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2773: return &safe_system ("curl $address -o$out >/dev/null 2>/dev/null");
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2774- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2912- #get PDB sequence
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2913: safe_system ("t_coffee -other_pg extract_from_pdb $pdb -seq >$outfile1");
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2914-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2916- $command="$pg $pdb simple.output > /dev/null 2>/dev/null";
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:2917: safe_system ($command);
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-2918-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-3008-
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:3009: &safe_system ("t_coffee -other_pg RNAplfold2tclib.pl -in=$seq -out=$lib");
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-3010-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-3033-
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:3034: safe_system ("x3dna-ssr -i=$pdb >/dev/null 2>/dev/null");
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-3035- if ( !-e $outfile)
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-3085-
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:3086: safe_system ("t_coffee -other_pg seq_reformat -in seq -in2 str -output vienna2tc_lib >$lib");
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-3087- if ( !-e $lib)
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-3228- close ($g);
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:3229: safe_system ("mv $fname $fname.old");
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-3230- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-3373- {
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:3374: `rm -rf $dir`;
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-3375- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-3461- if( $debug_generic_method ) { printf "~ exec: %s\n", $com; }
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:3462: exec ($com);
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-3463- if( $debug_generic_method ) { printf "~ exitcode: %s\n", $?; }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-3485-
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl:3486: return safe_system ($com, $ntry, ++$ctry);
t-coffee-13.41.0.28bdc39+dfsg/example/tc_generic_method.pl-3487- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-405-ull`;}\n elsif ( $alignpg eq \"muscle\")\n {\n \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:406: `$alignpg -in $seq > $msa 2>/dev/null`;\n }\n\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-407- elsif ( $alignpg eq \"clustalw\")\n {\n `$a\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-434-t_o`;\n }\n else\n {\n `cp $lmsa $seq\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:435:boot_o`;\n }\n\n if ($rmsa){`cp $seqboot_o\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-436- $rmsa`;}\n \n if ($tmode eq \"nj\" || $tmod\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-512-$nb_o`;\n unlink (\"outfile\");\n }\n\n\nelse\n\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:513: {\n `cp $msa $nb_o`;\n $n=2;\n }\n\nif ($\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-514-rmsa && -e $seqboot_o){print \"\\nOutput List of $\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:515:n Replicate MSA: $rmsa\\n\";`cp $seqboot_o $rmsa`;\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-516-}\nif ($rmat && -e $protdist_o){print \"\\nOutput \
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-519-\\nOutput List of $n Replicate TREES: $rtree\\n\";\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:520:`cp $nb_o $rtree`;}\n\n\n\n$con_o=&vtmpnam();\n$co\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-521-n_c=&vtmpnam();\nif ($n >1)\n {\n print \"Run \
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-526-rint \"[FAILED]\\n\";&my_exit (EXIT_FAILURE);}\n \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:527: `mv outtree $con_o`;\n unlink (\"outfile\");\\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:528:n }\nelse\n {\n `cp $nb_o $con_o`;\n }\n\n\n\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:529:`cp $con_o $out`;\nif ( !-e $out)\n {\n print \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-530-\"Tree Computation failed [FAILED]\\n\";\n &my_\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1014- }\n\n elsif ( $method eq \"muscle\")\n \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:1015:{\n `muscle -in seq.pep -out result.aln $param`;\n\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1016- }\n elsif ( $method eq \"probcons\")\n \
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1025-.pep > result.aln`;\n }\n\n else\n {\\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:1026:n `$method -infile=seq.pep -outfile=result.aln`;\n\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1027- }\n\n &set_temporary_dir (\"unset\",$mode\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1066- $c1 --pdb2 $id2 --chainid2 $c2 --email=$EMAIL >d\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:1067:ali_stderr 2>dali_stderr\";\n $dali=`$command`\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1068-;\n\n open (F, \"dali_stderr\");\n while (\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1188- my $p=shift (@ml);\n if ($p=~/::/)\n {\\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:1189:n if (safe_system (\"perl -M$p -e 1\")==$EXIT_SUCC\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1190-ESS){return 1;}\n else {return 0;}\n }\n e\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:1191:lse\n {\n $r=`which $p 2>/dev/null`;\n if ($r\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1192- eq \"\"){$r=0;}\n else {$r=1;}\n\n if ($r==0 && i\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1287-m} -t $h{1}{a3m} -tc $outfile.tmp -rank 1 -mapt 0 \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:1288:$param\";\n `$command`;\n\n # `hhalign -i $h{\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1289-0}{a3m} -t $h{1}{a3m} -tc $outfile.tmp -rank 1 -ma\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1302- $n);\n\n\n $i=$h{index};\n $aln=$h{aln};\n\\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:1303:n `cp $aln $$.hhh_aln`;\n $command=\"t_coffe\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1304-e -other_pg seq_reformat -in $aln -output hasch\";\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:1305:\n $hv=`$command`;chomp ($hv);\n\n $h{a2m}=\\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1306-"$tmp/$hv.tmp4hhpred.a2m\";\n $h{a3m}=\"$tmp/$h\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1317-h{a3m}\";\n myexit ($EXIT_FAILURE);\n }\n \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:1318: `buildali.pl $h{a3m} -n 1`;\n }\n\n\n \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:1319:$h{a2m_seq}=`head -n 2 $h{a2m} | grep -v \">\"`;ch\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1320-omp ($h{a2m_seq});\n $h{a3m_seq}=`head -n 2 $h{\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1329- grep \">\"`;\n $name=~/\\>(\\S+)/;\n $h{nam\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:1330:e}=$1;\n\n `cp $h{a2m} $i.a2m`;\n `cp $h{a3m\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:1331:} $i.a3m`;\n `cp $h{aln} $i.hh_aln`;\n\n ret\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1332-urn %h;\n }\nsub read_fasta_seq_index\n {\n m\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1787-ile $outfile -o xml>/dev/null 2>$error_log\";\n &\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:1788:safe_system ( $command);\n if (-e \"$outfile.xml\\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:1789:") {`mv $outfile.xml $outfile`;}\n }\n e\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1790-lse\n {\n if ($cl_method eq \"psiblast\"){$\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1831-ile.out.xml $outfile`;}\n elsif (-e \"$outfile.xm\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:1832:l.xml\"){`mv $outfile.xml.xml $outfile`;}\n elsif\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1833- (-e \"$outfile.out..xml\") {`mv $outfile.out..xml\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:1834: $outfile`;}\n elsif (-e \"$outfile.xml..xml\"){`\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1835-mv $outfile.xml..xml $outfile`;}\n else\n {\n \
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1852-\"$client -p $method -d $db -i $infile -o $outfile\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:1853: -m 7\";\n &safe_system ($command);\n }\n el\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1854-sif ( $SERVER eq \"LOCAL_blastall\")\n {\n &\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1857-l -d $db -i $infile -o $outfile -m7 -p blastp\";\n\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:1858: }\n &safe_system ($command);\n }\n el\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1859-sif ( $SERVER eq \"LOCAL\")\n {\n if ($ENV{\\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1865- with old blast commands\n ##\n $path=`which leg\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:1866:acy_blast.pl 2>/dev/null`; \n $path=`dirname $pa\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1867-th`; \n chomp($path);\n if ($method eq \"blas\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1878-th -p blastn -d $cl_db -i $infile -o $outfile -m7 \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:1879:-W6\";\n }\n &safe_system ($command);\n \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1880- }\n else\n {\n\n myexit(add_error (EXIT_FA\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1926-1_eq_fasta_file2($infile,$cache_file_infile)==1)\n\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:1927: {\n `cp $cache_file $outfile`;\n $CACHE_S\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1928-TATUS=\"READ CACHE\";\n return 1;\n }\n }\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1935-f (-e $outfile)\n {\n `cp $outfile $cache_fi\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:1936:le`;\n if ($cache_file_infile ne \"\"){ `cp $i\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-1937-nfile $cache_file_infile`;}\n\n #functions for\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-2263-ety check 1\n elsif (($dir=~/\\*/)){return ;}#s\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:2264:afety check 2\n else\n {\n `rm -rf $dir`;\\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-2265-n }\n return;\n }\nsub cleanup\n {\n \
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-2307- if( $debug_generic_method ) { printf \"~ exec: %s\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:2308:\\n\", $com; }\n exec ($com);\n if( $deb\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-2309-ug_generic_method ) { printf \"~ exitcode: %s\\n\"\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-3114-c $pdb $ref_file`));\n $pdb=lc($pdb);\n chomp(($va\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:3115:lue2=`grep -c $pdb $ref_file`));\n $value=($value1\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-3116- || $value2)?1:0;\n $value=($value>0)?1:0;\n \n re\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-3127-ubstr ($in,0, 4);\n $pdb=lc($pdb);\n \n chomp(($va\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:3128:lue=`grep $pdb $ref_file`));\n \n $value=~/^\\S+\\\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-3129-s+\\S+\\s+(\\S+)/;\n $ret=$1;\n if ( $ret eq\"\"){\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-3142-pdb $ref_file`));\n $pdb=lc($pdb);\n chomp((\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:3143:$value2=`grep -c $pdb $ref_file`));\n $value=($\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-3144-value1 || $value2)?1:0;\n $value=($value>0)?1:0\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-3357-tmp;}\n \n $file=~s/\\/\\//\\//g;\n if \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:3358: (-B $file && ($file=~/\\.Z/)) {`cp $file $tmp.Z`;\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:3359:`rm $tmp`;`gunzip $tmp.Z $SILENT`;$r=$tmp;}\n e\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-3360-lsif (-B $file && ($file=~/\\.gz/)){`cp $file $tmp\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:3361:.gz`;`gunzip $tmp.gz $SILENT`;return $r=$tmp;}\n \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:3362: elsif (-B $file ){`cp $file $tmp.gz`;`gunzip $tm\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-3363-p.gz $SILENT`;$r=$tmp;}\n elsif ( -e $file ) {$\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-3364-r= $file;}\n elsif ( -e \"$file.gz\" ){ `cp $fi\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:3365:le.gz $tmp.gz`;`gunzip $tmp.gz $SILENT`;$r=$tm\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-3366-p;} \n elsif ( -e \"$file.Z\") {`cp $file.Z \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:3367: $tmp.Z`; `gunzip $tmp.Z $SILENT`;$r=$tmp;}\n e\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-3368-lse {$r= $file;}\n\n if ( -e \"$tmp.Z\"){unlin\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-4391- print $g \"\\nDestroyed by $$\\n\";\n close \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:4392:($g);\n safe_system (\"mv $fname $fname.old\");\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-4393-\n }\n else\n {\n unlink ($fname);\n }\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-4460-\\*/)){return ;}#safety check 2\n else\n {\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:4461:\n `rm -rf $dir`;\n }\n return;\n }\nsub \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-4462-cleanup\n {\n #print stderr \"\\n----tc: $$ Ki\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-4536- \n my $p=shift (@ml);\n if ($p=~/::/)\n \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:4537: {\n if (safe_system (\"perl -M$p -e 1\")==$EXI\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-4538-T_SUCCESS){return 1;}\n else {return 0;}\n }\\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:4539:n else\n {\n $r=`which $p 2>/dev/null`;\n \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-4540-if ($r eq \"\"){return 0;}\n else {return 1;}\n \
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-4577-n }\n $pdb=substr ($in,0, 4);\n chomp((\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:4578:$value1=`grep -c $pdb $ref_file`));\n $pdb=lc($\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:4579:pdb);\n chomp(($value2=`grep -c $pdb $ref_file`\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-4580-));\n $value=($value1 || $value2)?1:0;\n $va\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-4711-IR && $ROOT_INSTALL){$INSTALL_DIR=\"/usr/local/bi\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:4712:n/\";}\n\nif (-d \"mcoffee\"){`cp mcoffee/* $TCM`;\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-4713-}\n\n\nour $ENV_FILE=\"$TCDIR/.t_coffee_env\";\nun\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-4755-clean/))\n {\n print \"------- cleaning execut\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:4756:ables -----\\n\";\n `rm bin/* $SILENT`;\n ex\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-4757-it ($EXIT_SUCCESS);\n }\n\nif ( !$PG{$target}){pr\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-4818-coffee/) ){print \"*------ Clean Installation Dire\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:4819:ctory: $BASE\\n\";`rm -rf $BASE`;}\nforeach my $pg\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-4820- (keys(%PG)){if ($PG{$pg}{install} && $PG{$pg}{sta\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-4910-r};\n }\n \n if ( $compil eq \"CPAN\")\\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:4911:n {\n if ( system (\"perl -M$p -e 1\")==$EXIT\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-4912-_SUCCESS){$ret=1;}\n else {$ret=0;}\n }\n \
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-4916-GINS_DIR/$p.exe\"){$ret=1;}\n else\n {\n $\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:4917:r=`which $p 2>/dev/null`;\n if ($r eq \"\"){$ret=0\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-4918-;}\n else {$ret=1;}\n }\n \n return $ret\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-4920-n my ($copied, $report);\n\n \n if (!$ROO\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:4921:T_INSTALL)\n {\n `$CP $BIN/* $PLUGINS_DIR`;\n\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-4922- if (-e \"$BIN/t_coffee\")\n {\n `$CP $BIN/t\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-4979- (!&pg_is_installed ($pg))\n {\n if ( $OS eq \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:4980:\"windows\"){`perl -M$compiler -e 'install $pg'`;}\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-4981-\n elsif ( $ROOT eq \"sudo\"){system (\"sudo perl \
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5016-, \"$wget_tmp\")==$EXIT_SUCCESS)\n {\n \n \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:5017: `mv $wget_tmp $distrib`;\n `$CP $distrib $DO\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5018-WNLOAD_DIR/`;\n }\n\n if (!-e $distrib)\n {\n \
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5063-_store(\"fsa\", \"$BIN/bin\");\n `mv $BIN/bin/* $B\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:5064:IN`;\n `rmdir $BIN/bin`;\n }\n \n #\n \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5065- # CLUSTALW module\n #\n elsif ($pg eq \"cl\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5066-ustalw\")\n {\n &flush_command(\"make $argume\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:5067:nts clustalw\");\n `$CP $pg $BIN $SILENT`;\n repo_\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5068-store($pg);\n }\n \n #\n # MAFFT mod\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5071-path (\"./mafft/bin\");\n mkpath (\"./mafft/lib\")\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:5072:;\n chdir \"$base/core\";\n `make clean $SILENT`;\\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5073-n &flush_command (\"make $arguments\");\n &flush_c\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5075-../mafft/bin\");\n \n #compile extension\n chdir \\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:5076:"$base/extensions\";\n `make clean $SILENT`;\n &fl\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5077-ush_command (\"make $arguments\");\n &flush_comman\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5087-IN`;\n }\n `tar -cvf mafft.tar mafft`;\n `gzip m\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:5088:afft.tar`;\n `mv mafft.tar.gz $BIN`;\n \n repo_sto\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5089-re(\"mafft/bin/mafft\", \"mafft/lib/\", \"$BIN/maf\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5114- {\n &add_C_libraries(\"./ProbabilisticModel.h\"\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:5115:, \"list\", \"cstring\");\n \n `rm *.exe $SILENT`;\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5116-\n &flush_command (\"make $arguments probcons\");\\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5122-es(\"./Main.cc\", \"iomanip\", \"cstring\",\"climi\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:5123:ts\");\n `rm *.exe $SILENT`;\n &flush_command (\"m\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5124-ake $arguments probcons\");\n &check_cp(\"probcons\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5209-source\";\n print \"\\n------- Compiling TMalig\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:5210:n\\n\";\n `rm TMalign TMalign.exe $SILENT`;\n \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5211- if ( $FC ne \"\"){&flush_command (\"make -i $PG{\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5247- chdir $TMP;\n \n if (!-e $name)\n {\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:5248:\n `rm x $SILENT`;\n if ( url2file(\"$download\",\\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:5249:"x\")==$EXIT_SUCCESS)\n {\n `mv x $name`;\n \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5250- }\n }\n \n if (!-e $name)\n {\n \
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5255-lling $pg\\n\";\n \n if ($name =~/tar\\.gz/)\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:5256:\n {\n `gunzip -f $name`;\n `tar -xvf $pg.ta\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:5257:r`;\n chdir $pg;\n `chmod u+x *`;\n `mv * $BIN`;\\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:5258:n #if (!($pg=~/\\*/)){`rm -rf $pg`;}\n }\n \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5259- else\n {\n &check_cp (\"$pg\", \"$BIN\");\n \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:5260:`chmod u+x $BIN/$pg`; \n unlink ($pg);\n }\n \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5261- chdir $base;\n $PG{$pg}{from_binary}=1;\n\n \
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5276- extract the package name from the specified path\\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:5277:n my $pg =`basename $_[0]`;\n chomp($pg);\n \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5278-\n my $VER = $PG{$pg}{version};\n my $CACHE \
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5282-e path if exists and create it again\n `rm -rf \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:5283:$CACHE`;\n `mkdir -p $CACHE`;\n \n for my $\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5284-path (@_) {\n\n # check if it is a single file\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:5285: \n if( -f $path ) {\n `cp $path $CACHE`;\n\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5286- }\n # .. or a directory, in this case copy all \
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5290- if( $_file ne \".\" && $_file ne \"..\") {\n \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:5291: `cp $path/$_file $CACHE`;\n }\n }\n } \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5292-\n } \n \n \n} \n\nsub repo_load \n{\n \
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5302-sitory cache. Using copy on path: $CACHE\\n\";\n \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:5303: `cp $CACHE/* $BIN`;\n return 1;\n}\n\nsub che\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5304-ck_file_list_exists \n {\n my ($base, @flist)=\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5307- return 1;\n }\nsub ls\n {\n my $f=@_[0];\\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:5308:n my @fl;\n chomp(@fl=`ls -1 $f`);\n retu\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5309-rn @fl;\n }\nsub flush_command\n {\n my $comm\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5341-t_run\n {\n my ($txt, $cmd)=(@_);\n \n i\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:5342:f ( system ($cmd)==$EXIT_SUCCESS){return $EXIT_SUC\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5343-CESS;}\n else \n {\n print \"------- $txt\\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5380-\//)\n {\n ($address, $name)=($download=~/(.*\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:5381:)\\/([^\\/]+)$/);\n `rm x $SILENT`;\n if (&url2fil\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-5382-e ($file,\"x\")==$EXIT_SUCCESS)\n {\n print \
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-6060-etic_penalty=0 -mocca_interactive -in $lib_name -i\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:6061:nfile $seq_file\";\n \n }\n\nsystem ($command);\\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-6062-n\nexit;\n\n","my $WSDL = 'http://www.ebi.ac.uk/To\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-7960-$cmd = \"RNAplfold -W $window_size < $fnametmp >/d\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:7961:ev/null\";\n system($cmd);\n \n if ($? !=\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-7962- 0) {\n printf STDERR \"ERROR: RNAplfold ($\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-8418-ir=~/\\*/)){return ;}#safety check 2\n else\n \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:8419: {\n `rm -rf $dir`;\n }\n return;\n }\\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-8420-nsub cleanup\n {\n #print stderr \"\\n----tc: \
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-8452-\n set_lock($$, \" -SHELL- $com (tcg)\");\n \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:8453: exec ($com);\n }\n else\n {\n lock\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-8454-4tc ($$, \"LLOCK\", \"LSET\", \"$pid\\n\");#update\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-8494-0;\n \n my $p=shift (@ml);\n if ($p=~/::/\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:8495:)\n {\n if (safe_system (\"perl -M$p -e 1\")=\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-8496-=$EXIT_SUCCESS){return 1;}\n else {return 0;}\n \
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-8555-ockholm formatted\n $cmd = \"sed -e '1d' $frawo\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:8556:ut\";\n system(\"$cmd > $fstk\");\n if ($? !\
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-8557-= 0) {\n $errmsg = \"command failed with ex\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-8911-y $n (keys (%h))\n {\n if ($test)\n {\n \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h:8912: system (\"cp $h{$n}{NFin} $h{$n}{NFout}\");\n \
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/perl_header_lib.h-8913- print \"$h{$n}{NFin} $h{$n}{NFout} $h{$n}{out}\\n\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/util_lib/util.c-2623-}
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/util_lib/util.c:2624:int print_param ( char *param, FILE *fp);
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/util_lib/util.c-2625-int print_param ( char *param, FILE *fp)
##############################################
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/util_lib/util.c-2654- if (!string) return 0;
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/util_lib/util.c:2655: //print_param (string, stdout);
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/util_lib/util.c:2656: //print_param (string, stderr);
t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source/util_lib/util.c-2657- va_start (ap, format);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/debian/README.Debian-13-To install all the necessary programs for running DM-COFFEE, you can run use
t-coffee-13.41.0.28bdc39+dfsg/debian/README.Debian:14:the option `~Rsuggests:^package$' of the `aptitude' package manager, or the
t-coffee-13.41.0.28bdc39+dfsg/debian/README.Debian-15-command `apt-get -o APT::Install-Suggests=true install'. In order to download
##############################################
t-coffee-13.41.0.28bdc39+dfsg/debian/patches/bypass_legacy_blast.patch-10-
t-coffee-13.41.0.28bdc39+dfsg/debian/patches/bypass_legacy_blast.patch:11: #&safe_system ("formatdb -i $db");
t-coffee-13.41.0.28bdc39+dfsg/debian/patches/bypass_legacy_blast.patch:12:- if ($blast eq "blastp"){&safe_system ("blastall -i $infile -d $db -m7 -p blastp -o io");}
t-coffee-13.41.0.28bdc39+dfsg/debian/patches/bypass_legacy_blast.patch:13:+ if ($blast eq "blastp"){&safe_system ("blastp -db $db -query $infile -out io -outfmt 5 -seg yes");}
t-coffee-13.41.0.28bdc39+dfsg/debian/patches/bypass_legacy_blast.patch:14: elsif ($blast eq "blastn"){&safe_system ("blastn -query $infile -db $db -outfmt 5 -word_size 4 -out io");}
t-coffee-13.41.0.28bdc39+dfsg/debian/patches/bypass_legacy_blast.patch-15-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/debian/patches/bypass_legacy_blast.patch-32- }
t-coffee-13.41.0.28bdc39+dfsg/debian/patches/bypass_legacy_blast.patch:33: &safe_system ($command);
t-coffee-13.41.0.28bdc39+dfsg/debian/patches/bypass_legacy_blast.patch-34- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/debian/patches/bypass_legacy_blast.patch-43-- $path=`which legacy_blast.pl 2>/dev/null`;
t-coffee-13.41.0.28bdc39+dfsg/debian/patches/bypass_legacy_blast.patch:44:- $path=`dirname $path`;
t-coffee-13.41.0.28bdc39+dfsg/debian/patches/bypass_legacy_blast.patch-45-- chomp($path);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/debian/patches/bypass_legacy_blast.patch-66- print "$command\n";
t-coffee-13.41.0.28bdc39+dfsg/debian/patches/bypass_legacy_blast.patch:67: &safe_system ($command);
t-coffee-13.41.0.28bdc39+dfsg/debian/patches/bypass_legacy_blast.patch-68-@@ -2859,7 +2853,7 @@ sub seq2tblastx_lib
##############################################
t-coffee-13.41.0.28bdc39+dfsg/debian/patches/ncbi-blast++_has_dropped_pl_extension.patch-166- sta.pl","fasta_seq2consan_aln.pl","clustalw_aln2fa\
t-coffee-13.41.0.28bdc39+dfsg/debian/patches/ncbi-blast++_has_dropped_pl_extension.patch:167:@@ -1789,7 +1789,7 @@ safe_system ( $command);\n if (-e \"$ou
t-coffee-13.41.0.28bdc39+dfsg/debian/patches/ncbi-blast++_has_dropped_pl_extension.patch:168: ") {`mv $outfile.xml $outfile`;}\n }\n e\
t-coffee-13.41.0.28bdc39+dfsg/debian/patches/ncbi-blast++_has_dropped_pl_extension.patch-169- lse\n {\n if ($cl_method eq \"psiblast\"){$\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/debian/patches/ncbi-blast++_has_dropped_pl_extension.patch-182- with old blast commands\n ##\n $path=`which leg\
t-coffee-13.41.0.28bdc39+dfsg/debian/patches/ncbi-blast++_has_dropped_pl_extension.patch:183: acy_blast.pl 2>/dev/null`; \n $path=`dirname $pa\
t-coffee-13.41.0.28bdc39+dfsg/debian/patches/ncbi-blast++_has_dropped_pl_extension.patch-184- th`; \n chomp($path);\n if ($method eq \"blas\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/debian/patches/ncbi-blast++_has_dropped_pl_extension.patch-201- th -p blastn -d $cl_db -i $infile -o $outfile -m7 \
t-coffee-13.41.0.28bdc39+dfsg/debian/patches/ncbi-blast++_has_dropped_pl_extension.patch:202: -W6\";\n }\n &safe_system ($command);\n \
t-coffee-13.41.0.28bdc39+dfsg/debian/patches/ncbi-blast++_has_dropped_pl_extension.patch-203- }\n else\n {\n\n myexit(add_error (EXIT_FA\
##############################################
t-coffee-13.41.0.28bdc39+dfsg/debian/tests/run-unit-test-6-if [ "$AUTOPKGTEST_TMP" = "" ] ; then
t-coffee-13.41.0.28bdc39+dfsg/debian/tests/run-unit-test:7: AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
t-coffee-13.41.0.28bdc39+dfsg/debian/tests/run-unit-test-8-fi
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-260- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:261: &safe_system ("t_coffee -other_pg fasta_seq2hmmtop_fasta.pl -in=seqfile -out=$lib_name -arch=$arch -psv=$psv");
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-262- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-492-
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:493: safe_system ("$hh -name=$s{$seq}{name} -method=search -db=$db -seq=seqfile -outfile=$profile_name");
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-494- if (-e $profile_name){$nseq=fasta2nseq($profile_name);}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-641-
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:642: my $value= &safe_system ("t_coffee -other_pg extract_from_pdb -model_type $pdb > $f");
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-643- my $r=&file2string ($f);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-653-
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:654: my $value= &safe_system ("t_coffee -other_pg extract_from_pdb -model_type $pdb > $f");
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-655- my $r=&file2string ($f);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-668-
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:669: $value= &safe_system ("t_coffee -other_pg extract_from_pdb -is_released_pdb_name $pdb > $f");
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-670- my $r=&file2string ($f);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-689-
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:690: #&safe_system ("formatdb -i $db");
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:691: if ($blast eq "blastp"){&safe_system ("blastall -i $infile -d $db -m7 -p blastp -o io");}
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:692: elsif ($blast eq "blastn"){&safe_system ("blastn -query $infile -db $db -outfmt 5 -word_size 4 -out io");}
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-693-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-759- }
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:760: &safe_system ("formatdb -i $infile");
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:761: &safe_system ("blastall -i $infile -d $infile -m7 -o io");
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-762- &set_blast_type ("io");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-833- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:834: `muscle -in seq.pep -out result.aln $param`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-835- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-845- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:846: `$method -d=seq.pep -o=result.aln -quiet 2>/dev/null`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-847- `mv result.aln.1.fas result.aln`;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-854- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:855: `$method -infile=seq.pep -outfile=result.aln`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-856- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-887- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:888: &safe_system ("$method -infile=seq.pep -pdbfile1=struc.pdb -outfile=result.aln $param>x 2>x");
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-889- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-914- $command="t_coffee -other_pg dalilite.pl --pdb1 $id1 --chainid1 $c1 --pdb2 $id2 --chainid2 $c2 --email=$EMAIL >dali_stderr 2>dali_stderr";
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:915: $dali=`$command`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-916-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-980- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:981: if ( &safe_system ("DaliLite -pairwise pdb1.pdb pdb2.pdb >tmp1")==$EXIT_SUCCESS)
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-982- {
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1016- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1017: if ( &safe_system ("TMalign pdb1.pdb pdb2.pdb >tmp1")==$EXIT_SUCCESS)
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1018- {
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1040- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1041: if ( &safe_system ("mustang -i pdb1.pdb pdb2.pdb -F fasta >/dev/null 2>/dev/null")==$EXIT_SUCCESS)
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1042- {
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1052- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1053: if ( &safe_system ("$method -pdbfile1=pdb1.pep -pdbfile2=pdb2.pdb -outfile=result.aln $param>x 2>x")==$EXIT_SUCCESS)
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1054- {
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1109-
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1110: safe_system("runsara.py $pdbfile1 $chain1 $pdbfile2 $chain2 -s -o $tmp_file --limitation 5000 > /dev/null 2> /dev/null");
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1111- if ($ENV{X3DNA_4_SARA}){$ENV{PATH}=$path;}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1149- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1150: `clustalw -profile1=$profile1 -profile2=$profile2 -outfile=$outfile`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1151- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1154-
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1155: `clustalo --p1 $profile1 --p2 $profile2 -o $outfile --force`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1156- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1162- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1163: `$method -profile1=$profile1 -profile2=$profile2 -outfile=$outfile $param> /dev/null 2>/dev/null`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1164- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1176- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1177: if (safe_system ("perl -M$p -e 1")==$EXIT_SUCCESS){return 1;}
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1178- else {return 0;}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1181- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1182: $r=`which $p 2>/dev/null`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1183- if ($r eq ""){$r=0;}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1209-
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1210: if (&pg_is_installed ("wget")){`wget www.google.com -O$tmp >/dev/null 2>/dev/null`;}
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1211: elsif (&pg_is_installed ("curl")){`curl www.google.com -o$tmp >/dev/null 2>/dev/null`;}
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1212-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1254- push (@TMPDIR_LIST, $tmp_dir);
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1255: `mkdir $tmp_dir`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1256- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1259- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1260: if (-e $list[$a]){ `cp $list[$a] $tmp_dir/$list[$a+1]`;}
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1261- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1276- chdir $initial_dir;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1277: # `t_coffee -other_pg seq_reformat -in $tmp_dir/$list[0] -output fasta_aln -out $tmp_dir/result2.aln`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1278: `cp $tmp_dir/$list[0] $tmp_dir/result2.aln`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1279- if ( $list[1] eq "stdout")
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1285- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1286: `mv $tmp_dir/result2.aln $list[1]`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1287- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1290- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1291: if (-e ("$tmp_dir/$f")){`mv $tmp_dir/$f .`;}
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1292- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1367-
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1368: safe_system ("$hh -method=align -profile1=$aln1 -profile2=$aln2 -outfile=$outfile");
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1369- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1400- $command="hhalign -i $h{0}{a3m} -t $h{1}{a3m} -tc $outfile.tmp -rank 1 -mapt 0 $param";
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1401: `$command`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1402-
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1403: # `hhalign -i $h{0}{a3m} -t $h{1}{a3m} -tc $outfile.tmp -rank 1 -mapt 0 -gapf 0.8 -gapg 0.8`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1404-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1436-
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1437: `cp $aln $$.hhh_aln`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1438- $command="t_coffee -other_pg seq_reformat -in $aln -output hasch";
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1439: $hv=`$command`;chomp ($hv);
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1440-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1446- $x=`which hhconsensus`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1447: `hhconsensus -M 50 -i $h{aln} -oa2m $h{a2m}`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1448- if (!-e $h{a2m})
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1453-
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1454: `hhconsensus -M 50 -i $h{aln} -oa3m $h{a3m}`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1455- if (!-e $h{a3m})
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1459- }
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1460: `buildali.pl $h{a3m} -n 1`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1461- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1463-
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1464: $h{a2m_seq}=`head -n 2 $h{a2m} | grep -v ">"`;chomp ($h{a2m_seq});
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1465: $h{a3m_seq}=`head -n 2 $h{a3m} | grep -v ">"`;chomp ($h{a3m_seq});
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1466- $h{cons}=$h{a2m_seq};
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1467: $h{seq}=`head -n 2 $h{aln} | grep -v ">"`;chomp ($h{seq});
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1468-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1485-
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1486: $name=`head -n 2 $h{aln} | grep ">"`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1487- $name=~/\>(\S+)/;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1489-
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1490: `cp $h{a2m} $i.a2m`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1491: `cp $h{a3m} $i.a3m`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:1492: `cp $h{aln} $i.hh_aln`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-1493-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2308- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2309: &safe_system ("t_coffee -other_pg seq_reformat -in $tmp -action +trim _aln_n$trim\_K1 -output fasta_aln -out $outfile");
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2310- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2312- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2313: &safe_system ("t_coffee -other_pg seq_reformat -in $tmp -action +trim _aln_%%$trim\_K1 -output fasta_aln -out $outfile");
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2314- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2317- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2318: &safe_system ("mv $tmp $outfile");
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2319- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2399-
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2400: `gorIV -prd $infile -seq $gor_seq -obs $gor_obs > gor_tmp`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2401- open (GR, ">$outfile");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2451- print "\tPSITM: kept $p{n} Homologues for Sequence $p{0}{name}\n";
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2452: &safe_system ("t_coffee -other_pg fasta_seq2hmmtop_fasta.pl -in=tm_input -out=$outfile -output=cons -cov=70 -trim=95 -arch=$arch -psv=$psv");
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2453- unlink ("tm_input");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2493- print "\tGORTM: kept $p{n} Homologues for Sequence $p{0}{name}\n";
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2494: &safe_system ("t_coffee -other_pg fasta_seq2hmmtop_fasta.pl -in=gor_input -out=$outfile -output=cons -cov=70 -trim=95 -gor_seq=$gor_seq -gor_obs=$gor_obs -mode=gor");
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2495- unlink ("tm_input");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2529- $command="t_coffee -other_pg wublast.pl --email $EMAIL $infile -D $db -p $cl_method --outfile $outfile -o xml>/dev/null 2>$error_log";
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2530: &safe_system ( $command);
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2531: if (-e "$outfile.xml") {`mv $outfile.xml $outfile`;}
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2532- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2537- $command="t_coffee -other_pg blastpgp.pl --email $EMAIL $infile -d $db --outfile $outfile -p $cl_method --mode PSI-Blast>/dev/null 2>$error_log";
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2538: &safe_system ( $command);
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2539-
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2540: if (-e "$outfile.xml") {`mv $outfile.xml $outfile`;}
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2541- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2562- }
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2563: &safe_system ( $command,5);
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2564: if (-e "$outfile.out.xml") {`mv $outfile.out.xml $outfile`;}
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2565: elsif (-e "$outfile.xml.xml"){`mv $outfile.xml.xml $outfile`;}
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2566: elsif (-e "$outfile.out..xml") {`mv $outfile.out..xml $outfile`;}
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2567: elsif (-e "$outfile.xml..xml"){`mv $outfile.xml..xml $outfile`;}
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2568- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2586- $command="$cl_method -db $cl_db -query $infile -out $outfile -outfmt 5 -remote";
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2587: &safe_system ($command);
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2588- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2592- $command="$client -p $method -d $db -i $infile -o $outfile -m 7";
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2593: &safe_system ($command);
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2594- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2601- }
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2602: &safe_system ($command);
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2603- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2618- $path=`which legacy_blast.pl 2>/dev/null`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2619: $path=`dirname $path`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2620- chomp($path);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2635- print "$command\n";
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2636: &safe_system ($command);
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2637- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2683- &cache_file("SET",$infile,$name,$method,$db,$outfile,$SERVER);
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2684: #system ("cp $outfile ~/Dropbox/tmp/cedric.out");
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2685- #die;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2722- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2723: `cp $cache_file $outfile`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2724- $CACHE_STATUS="READ CACHE";
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2738- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2739: `cp $outfile $cache_file`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2740: if ($cache_file_infile ne ""){ `cp $infile $cache_file_infile`;}
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2741-
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2742- #functions for updating the cache
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2743: #`t_coffee -other_pg clean_cache.pl -file $cache_file_sh -dir $CACHE`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2744: #`t_coffee -other_pg clean_cache.pl -file $cache_file_infile_sh -dir $CACHE`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2745- return 1;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2757- elsif ( !-e $f2){return 0;}
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2758: elsif ($f1 eq "" || $f2 eq "" || `diff $f1 $f2` eq ""){return 1;}
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2759-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2774- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2775: return &safe_system ("wget $address -O$out >/dev/null 2>/dev/null");
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2776- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2778- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2779: return &safe_system ("curl $address -o$out >/dev/null 2>/dev/null");
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2780- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2918- #get PDB sequence
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2919: safe_system ("t_coffee -other_pg extract_from_pdb $pdb -seq >$outfile1");
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2920-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2922- $command="$pg $pdb simple.output > /dev/null 2>/dev/null";
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:2923: safe_system ($command);
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-2924-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-3014-
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:3015: &safe_system ("t_coffee -other_pg RNAplfold2tclib.pl -in=$seq -out=$lib");
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-3016-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-3039-
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:3040: safe_system ("x3dna-ssr -i=$pdb >/dev/null 2>/dev/null");
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-3041- if ( !-e $outfile)
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-3091-
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:3092: safe_system ("t_coffee -other_pg seq_reformat -in seq -in2 str -output vienna2tc_lib >$lib");
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-3093- if ( !-e $lib)
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-3234- close ($g);
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:3235: safe_system ("mv $fname $fname.old");
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-3236- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-3379- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:3380: `rm -rf $dir`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-3381- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-3467- if( $debug_generic_method ) { printf "~ exec: %s\n", $com; }
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:3468: exec ($com);
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-3469- if( $debug_generic_method ) { printf "~ exitcode: %s\n", $?; }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-3491-
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl:3492: return safe_system ($com, $ntry, ++$ctry);
t-coffee-13.41.0.28bdc39+dfsg/.pc/bypass_legacy_blast.patch/example/tc_generic_method.pl-3493- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/set_proper_dir_permissions.patch/t_coffee_source/util_lib/util.c-2623-}
t-coffee-13.41.0.28bdc39+dfsg/.pc/set_proper_dir_permissions.patch/t_coffee_source/util_lib/util.c:2624:int print_param ( char *param, FILE *fp);
t-coffee-13.41.0.28bdc39+dfsg/.pc/set_proper_dir_permissions.patch/t_coffee_source/util_lib/util.c-2625-int print_param ( char *param, FILE *fp)
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/set_proper_dir_permissions.patch/t_coffee_source/util_lib/util.c-2654- if (!string) return 0;
t-coffee-13.41.0.28bdc39+dfsg/.pc/set_proper_dir_permissions.patch/t_coffee_source/util_lib/util.c:2655: //print_param (string, stdout);
t-coffee-13.41.0.28bdc39+dfsg/.pc/set_proper_dir_permissions.patch/t_coffee_source/util_lib/util.c:2656: //print_param (string, stderr);
t-coffee-13.41.0.28bdc39+dfsg/.pc/set_proper_dir_permissions.patch/t_coffee_source/util_lib/util.c-2657- va_start (ap, format);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/mayhem.patch/t_coffee_source/util_lib/util.c-2623-}
t-coffee-13.41.0.28bdc39+dfsg/.pc/mayhem.patch/t_coffee_source/util_lib/util.c:2624:int print_param ( char *param, FILE *fp);
t-coffee-13.41.0.28bdc39+dfsg/.pc/mayhem.patch/t_coffee_source/util_lib/util.c-2625-int print_param ( char *param, FILE *fp)
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/mayhem.patch/t_coffee_source/util_lib/util.c-2654- if (!string) return 0;
t-coffee-13.41.0.28bdc39+dfsg/.pc/mayhem.patch/t_coffee_source/util_lib/util.c:2655: //print_param (string, stdout);
t-coffee-13.41.0.28bdc39+dfsg/.pc/mayhem.patch/t_coffee_source/util_lib/util.c:2656: //print_param (string, stderr);
t-coffee-13.41.0.28bdc39+dfsg/.pc/mayhem.patch/t_coffee_source/util_lib/util.c-2657- va_start (ap, format);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-203-#prepare mcoffee files [Only if vanilla installation]
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:204:if (-d "mcoffee"){`cp mcoffee/* $TCM`;}
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-205-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-304- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:305: `rm $BIN/$pg $BIN/$pg.exe $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-306- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-313- print "------- cleaning executables -----\n";
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:314: `rm bin/* $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-315- exit ($EXIT_SUCCESS);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-402-
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:403:if ($clean==1 && ($BASE=~/install4tcoffee/) ){print "*------ Clean Installation Directory: $BASE\n";`rm -rf $BASE`;}
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-404-#failure if one program was not well installed
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-568- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:569: if ( system ("perl -M$p -e 1")==$EXIT_SUCCESS){$ret=1;}
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-570- else {$ret=0;}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-579- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:580: $r=`which $p 2>/dev/null`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-581- if ($r eq ""){$ret=0;}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-594- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:595: `$CP $BIN/* $PLUGINS_DIR`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-596- if (-e "$BIN/t_coffee")
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-597- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:598: `$CP $BIN/t_coffee $INSTALL_DIR`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-599- unlink("$PLUGINS_DIR/t_coffee");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-711- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:712: if ( $OS eq "windows"){`perl -M$compiler -e 'install $pg'`;}
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:713: elsif ( $ROOT eq "sudo"){system ("sudo perl -M$compiler -e 'install $pg'");}
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:714: else {system ("su root -c perl -M$compiler -e 'install $pg'");}
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-715- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-767- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:768: `$CP $DOWNLOAD_DIR/$distrib .`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-769- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-778-
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:779: `mv $wget_tmp $distrib`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:780: `$CP $distrib $DOWNLOAD_DIR/`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-781- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-817- print "\n------- Compiling/Installing $pg\n";
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:818: `make clean $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-819-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-838- #old style distribution
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:839: `rm *.o sap sap.exe ./util/aa/*.o ./util/wt/.o $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-840- &flush_command ("make $arguments sap");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-887- repo_store("fsa", "$BIN/bin");
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:888: `mv $BIN/bin/* $BIN`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:889: `rmdir $BIN/bin`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-890- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-897- &flush_command("make $arguments clustalw");
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:898: `$CP $pg $BIN $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-899- repo_store($pg);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-913- chdir "$base/core";
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:914: `make clean $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-915- &flush_command ("make $arguments");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-919- chdir "$base/extensions";
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:920: `make clean $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-921- &flush_command ("make $arguments");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-931- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:932: `$CP mafft/lib/* $BIN`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:933: `$CP mafft/bin/mafft $BIN`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-934- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-936- `gzip mafft.tar`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:937: `mv mafft.tar.gz $BIN`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-938-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-996-
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:997: `rm *.exe $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-998- &flush_command ("make $arguments probcons");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1009- &add_C_libraries("./Main.cc", "iomanip", "cstring","climits");
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:1010: `rm *.exe $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1011- &flush_command ("make $arguments probcons");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1020- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:1021: `rm *.o muscle muscle.exe $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1022- if ($OS eq "macosx" || $OS eq "linux")
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1041- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:1042: `rm *.o muscle muscle.exe $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1043- &flush_command ("./mk");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1078- &add_C_libraries("./Amap.cc", "iomanip", "cstring","climits");
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:1079: `make clean $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1080- &flush_command ("make $arguments all");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1182- print "\n------- Compiling TMalign\n";
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:1183: `rm TMalign TMalign.exe $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1184- if ( $FC ne ""){&flush_command ("make -i $PG{Fortran}{arguments} TMalign");}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1251- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:1252: `rm x $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1253- if ( url2file("$download","x")==$EXIT_SUCCESS)
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1254- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:1255: `mv x $name`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1256- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1269- {
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:1270: `gunzip -f $name`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:1271: `tar -xvf $pg.tar`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1272- chdir $pg;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1273- `chmod u+x *`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:1274: `mv * $BIN`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:1275: #if (!($pg=~/\*/)){`rm -rf $pg`;}
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1276- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1279- &check_cp ("$pg", "$BIN");
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:1280: `chmod u+x $BIN/$pg`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1281- unlink ($pg);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1330-
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:1331: `$CP $from $to`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1332- return 1;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1347- # extract the package name from the specified path
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:1348: my $pg =`basename $_[0]`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1349- chomp($pg);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1356- # clean the cache path if exists and create it again
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:1357: `rm -rf $CACHE`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:1358: `mkdir -p $CACHE`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1359-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1363- if( -f $path ) {
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:1364: `cp $path $CACHE`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1365- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1373- if( $_file ne "." && $_file ne "..") {
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:1374: `cp $path/$_file $CACHE`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1375- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1403- print "-------- Module \"$pg\" found on repository cache. Using copy on path: $CACHE\n";
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:1404: `cp $CACHE/* $BIN`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1405- return 1;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1422- my @fl;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:1423: chomp(@fl=`ls -1 $f`);
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1424- return @fl;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1495-
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:1496: if ( system ($cmd)==$EXIT_SUCCESS){return $EXIT_SUCCESS;}
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1497- else
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1499- print "------- $txt\n";
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:1500: if ( $ROOT eq "sudo"){return system ("sudo $cmd");}
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:1501: else {return system ("su root -c \"$cmd\"");}
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1502- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1599- ($address, $name)=($download=~/(.*)\/([^\/]+)$/);
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:1600: `rm x $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1601- if (&url2file ($file,"x")==$EXIT_SUCCESS)
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1603- print "------- Susscessful upload of $name";
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:1604: `mv x $name`;
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-1605- $file=$name;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-2133-
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:2134: system ("mv $file $file.old");
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-2135- open ($O, ">$file");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-2158-
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install:2159: system ("mv $file $file.old");
t-coffee-13.41.0.28bdc39+dfsg/.pc/clustalw2.patch/install-2160- open ($O, ">$file");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-203-#prepare mcoffee files [Only if vanilla installation]
t-coffee-13.41.0.28bdc39+dfsg/install:204:if (-d "mcoffee"){`cp mcoffee/* $TCM`;}
t-coffee-13.41.0.28bdc39+dfsg/install-205-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-304- {
t-coffee-13.41.0.28bdc39+dfsg/install:305: `rm $BIN/$pg $BIN/$pg.exe $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/install-306- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-313- print "------- cleaning executables -----\n";
t-coffee-13.41.0.28bdc39+dfsg/install:314: `rm bin/* $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/install-315- exit ($EXIT_SUCCESS);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-402-
t-coffee-13.41.0.28bdc39+dfsg/install:403:if ($clean==1 && ($BASE=~/install4tcoffee/) ){print "*------ Clean Installation Directory: $BASE\n";`rm -rf $BASE`;}
t-coffee-13.41.0.28bdc39+dfsg/install-404-#failure if one program was not well installed
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-568- {
t-coffee-13.41.0.28bdc39+dfsg/install:569: if ( system ("perl -M$p -e 1")==$EXIT_SUCCESS){$ret=1;}
t-coffee-13.41.0.28bdc39+dfsg/install-570- else {$ret=0;}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-579- {
t-coffee-13.41.0.28bdc39+dfsg/install:580: $r=`which $p 2>/dev/null`;
t-coffee-13.41.0.28bdc39+dfsg/install-581- if ($r eq ""){$ret=0;}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-594- {
t-coffee-13.41.0.28bdc39+dfsg/install:595: `$CP $BIN/* $PLUGINS_DIR`;
t-coffee-13.41.0.28bdc39+dfsg/install-596- if (-e "$BIN/t_coffee")
t-coffee-13.41.0.28bdc39+dfsg/install-597- {
t-coffee-13.41.0.28bdc39+dfsg/install:598: `$CP $BIN/t_coffee $INSTALL_DIR`;
t-coffee-13.41.0.28bdc39+dfsg/install-599- unlink("$PLUGINS_DIR/t_coffee");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-711- {
t-coffee-13.41.0.28bdc39+dfsg/install:712: if ( $OS eq "windows"){`perl -M$compiler -e 'install $pg'`;}
t-coffee-13.41.0.28bdc39+dfsg/install:713: elsif ( $ROOT eq "sudo"){system ("sudo perl -M$compiler -e 'install $pg'");}
t-coffee-13.41.0.28bdc39+dfsg/install:714: else {system ("su root -c perl -M$compiler -e 'install $pg'");}
t-coffee-13.41.0.28bdc39+dfsg/install-715- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-767- {
t-coffee-13.41.0.28bdc39+dfsg/install:768: `$CP $DOWNLOAD_DIR/$distrib .`;
t-coffee-13.41.0.28bdc39+dfsg/install-769- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-778-
t-coffee-13.41.0.28bdc39+dfsg/install:779: `mv $wget_tmp $distrib`;
t-coffee-13.41.0.28bdc39+dfsg/install:780: `$CP $distrib $DOWNLOAD_DIR/`;
t-coffee-13.41.0.28bdc39+dfsg/install-781- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-817- print "\n------- Compiling/Installing $pg\n";
t-coffee-13.41.0.28bdc39+dfsg/install:818: `make clean $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/install-819-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-838- #old style distribution
t-coffee-13.41.0.28bdc39+dfsg/install:839: `rm *.o sap sap.exe ./util/aa/*.o ./util/wt/.o $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/install-840- &flush_command ("make $arguments sap");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-887- repo_store("fsa", "$BIN/bin");
t-coffee-13.41.0.28bdc39+dfsg/install:888: `mv $BIN/bin/* $BIN`;
t-coffee-13.41.0.28bdc39+dfsg/install:889: `rmdir $BIN/bin`;
t-coffee-13.41.0.28bdc39+dfsg/install-890- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-897- &flush_command("make $arguments clustalw");
t-coffee-13.41.0.28bdc39+dfsg/install:898: `$CP $pg $BIN $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/install-899- repo_store($pg);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-913- chdir "$base/core";
t-coffee-13.41.0.28bdc39+dfsg/install:914: `make clean $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/install-915- &flush_command ("make $arguments");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-919- chdir "$base/extensions";
t-coffee-13.41.0.28bdc39+dfsg/install:920: `make clean $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/install-921- &flush_command ("make $arguments");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-931- {
t-coffee-13.41.0.28bdc39+dfsg/install:932: `$CP mafft/lib/* $BIN`;
t-coffee-13.41.0.28bdc39+dfsg/install:933: `$CP mafft/bin/mafft $BIN`;
t-coffee-13.41.0.28bdc39+dfsg/install-934- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-936- `gzip mafft.tar`;
t-coffee-13.41.0.28bdc39+dfsg/install:937: `mv mafft.tar.gz $BIN`;
t-coffee-13.41.0.28bdc39+dfsg/install-938-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-996-
t-coffee-13.41.0.28bdc39+dfsg/install:997: `rm *.exe $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/install-998- &flush_command ("make $arguments probcons");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-1009- &add_C_libraries("./Main.cc", "iomanip", "cstring","climits");
t-coffee-13.41.0.28bdc39+dfsg/install:1010: `rm *.exe $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/install-1011- &flush_command ("make $arguments probcons");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-1020- {
t-coffee-13.41.0.28bdc39+dfsg/install:1021: `rm *.o muscle muscle.exe $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/install-1022- if ($OS eq "macosx" || $OS eq "linux")
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-1041- {
t-coffee-13.41.0.28bdc39+dfsg/install:1042: `rm *.o muscle muscle.exe $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/install-1043- &flush_command ("./mk");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-1078- &add_C_libraries("./Amap.cc", "iomanip", "cstring","climits");
t-coffee-13.41.0.28bdc39+dfsg/install:1079: `make clean $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/install-1080- &flush_command ("make $arguments all");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-1182- print "\n------- Compiling TMalign\n";
t-coffee-13.41.0.28bdc39+dfsg/install:1183: `rm TMalign TMalign.exe $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/install-1184- if ( $FC ne ""){&flush_command ("make -i $PG{Fortran}{arguments} TMalign");}
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-1251- {
t-coffee-13.41.0.28bdc39+dfsg/install:1252: `rm x $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/install-1253- if ( url2file("$download","x")==$EXIT_SUCCESS)
t-coffee-13.41.0.28bdc39+dfsg/install-1254- {
t-coffee-13.41.0.28bdc39+dfsg/install:1255: `mv x $name`;
t-coffee-13.41.0.28bdc39+dfsg/install-1256- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-1269- {
t-coffee-13.41.0.28bdc39+dfsg/install:1270: `gunzip -f $name`;
t-coffee-13.41.0.28bdc39+dfsg/install:1271: `tar -xvf $pg.tar`;
t-coffee-13.41.0.28bdc39+dfsg/install-1272- chdir $pg;
t-coffee-13.41.0.28bdc39+dfsg/install-1273- `chmod u+x *`;
t-coffee-13.41.0.28bdc39+dfsg/install:1274: `mv * $BIN`;
t-coffee-13.41.0.28bdc39+dfsg/install:1275: #if (!($pg=~/\*/)){`rm -rf $pg`;}
t-coffee-13.41.0.28bdc39+dfsg/install-1276- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-1279- &check_cp ("$pg", "$BIN");
t-coffee-13.41.0.28bdc39+dfsg/install:1280: `chmod u+x $BIN/$pg`;
t-coffee-13.41.0.28bdc39+dfsg/install-1281- unlink ($pg);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-1330-
t-coffee-13.41.0.28bdc39+dfsg/install:1331: `$CP $from $to`;
t-coffee-13.41.0.28bdc39+dfsg/install-1332- return 1;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-1347- # extract the package name from the specified path
t-coffee-13.41.0.28bdc39+dfsg/install:1348: my $pg =`basename $_[0]`;
t-coffee-13.41.0.28bdc39+dfsg/install-1349- chomp($pg);
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-1356- # clean the cache path if exists and create it again
t-coffee-13.41.0.28bdc39+dfsg/install:1357: `rm -rf $CACHE`;
t-coffee-13.41.0.28bdc39+dfsg/install:1358: `mkdir -p $CACHE`;
t-coffee-13.41.0.28bdc39+dfsg/install-1359-
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-1363- if( -f $path ) {
t-coffee-13.41.0.28bdc39+dfsg/install:1364: `cp $path $CACHE`;
t-coffee-13.41.0.28bdc39+dfsg/install-1365- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-1373- if( $_file ne "." && $_file ne "..") {
t-coffee-13.41.0.28bdc39+dfsg/install:1374: `cp $path/$_file $CACHE`;
t-coffee-13.41.0.28bdc39+dfsg/install-1375- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-1403- print "-------- Module \"$pg\" found on repository cache. Using copy on path: $CACHE\n";
t-coffee-13.41.0.28bdc39+dfsg/install:1404: `cp $CACHE/* $BIN`;
t-coffee-13.41.0.28bdc39+dfsg/install-1405- return 1;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-1422- my @fl;
t-coffee-13.41.0.28bdc39+dfsg/install:1423: chomp(@fl=`ls -1 $f`);
t-coffee-13.41.0.28bdc39+dfsg/install-1424- return @fl;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-1495-
t-coffee-13.41.0.28bdc39+dfsg/install:1496: if ( system ($cmd)==$EXIT_SUCCESS){return $EXIT_SUCCESS;}
t-coffee-13.41.0.28bdc39+dfsg/install-1497- else
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-1499- print "------- $txt\n";
t-coffee-13.41.0.28bdc39+dfsg/install:1500: if ( $ROOT eq "sudo"){return system ("sudo $cmd");}
t-coffee-13.41.0.28bdc39+dfsg/install:1501: else {return system ("su root -c \"$cmd\"");}
t-coffee-13.41.0.28bdc39+dfsg/install-1502- }
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-1599- ($address, $name)=($download=~/(.*)\/([^\/]+)$/);
t-coffee-13.41.0.28bdc39+dfsg/install:1600: `rm x $SILENT`;
t-coffee-13.41.0.28bdc39+dfsg/install-1601- if (&url2file ($file,"x")==$EXIT_SUCCESS)
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-1603- print "------- Susscessful upload of $name";
t-coffee-13.41.0.28bdc39+dfsg/install:1604: `mv x $name`;
t-coffee-13.41.0.28bdc39+dfsg/install-1605- $file=$name;
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-2124-
t-coffee-13.41.0.28bdc39+dfsg/install:2125: system ("mv $file $file.old");
t-coffee-13.41.0.28bdc39+dfsg/install-2126- open ($O, ">$file");
##############################################
t-coffee-13.41.0.28bdc39+dfsg/install-2149-
t-coffee-13.41.0.28bdc39+dfsg/install:2150: system ("mv $file $file.old");
t-coffee-13.41.0.28bdc39+dfsg/install-2151- open ($O, ">$file");