[med-svn] r17756 - trunk/packages/t-coffee/trunk/debian/patches
Andreas Tille
tille at moszumanska.debian.org
Sat Aug 16 19:18:47 UTC 2014
Author: tille
Date: 2014-08-16 19:18:47 +0000 (Sat, 16 Aug 2014)
New Revision: 17756
Modified:
trunk/packages/t-coffee/trunk/debian/patches/ncbi-blast++_has_dropped_pl_extension.patch
Log:
Update patches
Modified: trunk/packages/t-coffee/trunk/debian/patches/ncbi-blast++_has_dropped_pl_extension.patch
===================================================================
--- trunk/packages/t-coffee/trunk/debian/patches/ncbi-blast++_has_dropped_pl_extension.patch 2014-08-16 06:36:12 UTC (rev 17755)
+++ trunk/packages/t-coffee/trunk/debian/patches/ncbi-blast++_has_dropped_pl_extension.patch 2014-08-16 19:18:47 UTC (rev 17756)
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-LastChanged: Fri, 29 Nov 2013 10:27:47 +0100
+Last-Update: Sat, 16 Aug 2014 21:13:18 +0200
BugsDebian: http://bugs.debian.org/730722
Description: Cope with renaming of scripts in ncbi-blast++
Since ncbi-blast++ has renamed some perl scripts according to
@@ -7,9 +7,9 @@
s/legacy_blast\.pl/legacy_blast/
s/blastpgp\.pl/blastpgp/
---- a/t_coffee_source/define_header.h
-+++ b/t_coffee_source/define_header.h
-@@ -651,7 +651,7 @@
+--- T-COFFEE_distribution_Version_11.00.8cbe486.orig/t_coffee_source/programmes_define.h
++++ T-COFFEE_distribution_Version_11.00.8cbe486/t_coffee_source/programmes_define.h
+@@ -309,7 +309,7 @@
#define EBIWUBLASTc_source "empty"
#define EBIWUBLASTc_update_action "never"
#define EBIWUBLASTc_mode "psicoffee,expresso,accurate"
@@ -18,7 +18,7 @@
#define EBIBLASTPGPc_type "protein_homology_predictor"
#define EBIBLASTPGPc_ADDRESS "built_in"
#define EBIBLASTPGPc_ADDRESS2 "http://www.ebi.ac.uk/Tools/webservices/services/blastpgp"
-@@ -676,7 +676,7 @@
+@@ -326,7 +326,7 @@
#define blastall_source "empty"
#define blastall_update_action "never"
#define blastall_mode "psicoffee,expresso,3dcoffee"
@@ -27,110 +27,9 @@
#define NCBIBLAST_type "protein_homology_predictor"
#define NCBIBLAST_ADDRESS "ftp://ftp.ncbi.nih.gov/blast/executables/LATEST"
#define NCBIBLAST_language "C"
---- a/t_coffee_source/perl_header_lib.h
-+++ b/t_coffee_source/perl_header_lib.h
-@@ -4,7 +4,7 @@ msa2bootstrap.pl","t_coffee_dpa","t_coff
- tc_generic_method.pl","generic_method.tc_method","\
- clustalw_method.tc_method","extract_from_pdb","ins\
- tall.pl","clean_cache.pl","nature_protocol.pl","mo\
--cca","dalilite.pl","wublast.pl","blastpgp.pl","ncb\
-+cca","dalilite.pl","wublast.pl","blastpgp","ncb\
- iblast_lwp.pl","wublast_lwp.pl","RNAplfold2tclib.p\
- l","fasta_seq2RNAplfold_templatefile.pl","fasta_se\
- q2hmmtop_fasta.pl","fasta_seq2consan_aln.pl","clus\
-@@ -2379,7 +2379,7 @@ se lock\n\n if ( $debug_lock ){print
- ;\n }\n\nsub blast_com2new_blast_com\n {\n \
- my $com=shift;\n if ($ENV{\"NCBI_BLAST_4_TC\
- OFFEE\"} eq \"OLD\"){return $com;}\n elsif (!\
--&pg_is_installed(\"legacy_blast.pl\")){return $com\
-+&pg_is_installed(\"legacy_blast\")){return $com\
- ;}\n else\n {\n if ($com=~/formatdb/)\n \
- {\n $com=~s/formatdb/makeblastdb/;\n \
- $com=~s/\\-i/\\-in/;\n if ($com =~/pF/){$com\
-@@ -2390,13 +2390,13 @@ n }\n elsif ($com =~/^blastn/){ret
- \n elsif (&is_blast_package($com))\n {\n \
- my $path;\n\n if ( $ENV{\"NCBI_BIN_4_TCOF\
- FEE\"}){$path=$ENV{\"NCBI_BLAST_4_TCOFFEE\"};}\n \
-- else\n {\n $path=`which legacy_blast.pl`;\
-+ else\n {\n $path=`which legacy_blast`;\
- \n $path=~s/\\/legacy_blast\\.pl//;\n chomp \
- ($path);\n }\n $path=\"--path $path\";\n \
- if ( $com=~/\\>\\>/){$com=~s/\\>\\>/ $path \\>\
- \\>/;}\n elsif ( $com=~/\\>/){$com=~s/\\>/ $\
- path \\>/;}\n else {$com.=\" $path\";}\n \
-- $com=\"legacy_blast.pl $com\";\n\n return\
-+ $com=\"legacy_blast $com\";\n\n return\
- $com;\n }\n }\n }\nsub safe_system\n{\n m\
- y $com=shift;\n my $ntry=shift;\n my $ctry=shift\
- ;\n my $pid;\n my $status;\n my $ppid=getppid()\
-@@ -5571,16 +5571,16 @@ ervices/wublast\";\n$PG{\"wublast.pl\"}{
- \"Perl\";\n$PG{\"wublast.pl\"}{\"source\"}=\"empty\
- \";\n$PG{\"wublast.pl\"}{\"update_action\"}=\"neve\
- r\";\n$PG{\"wublast.pl\"}{\"mode\"}=\"psicoffee,ex\
--presso,accurate\";\n$PG{\"blastpgp.pl\"}{\"4_TCOFF\
--EE\"}=\"EBIBLASTPGPc\";\n$PG{\"blastpgp.pl\"}{\"ty\
-+presso,accurate\";\n$PG{\"blastpgp\"}{\"4_TCOFF\
-+EE\"}=\"EBIBLASTPGPc\";\n$PG{\"blastpgp\"}{\"ty\
- pe\"}=\"protein_homology_predictor\";\n$PG{\"blast\
- pgp.pl\"}{\"ADDRESS\"}=\"built_in\";\n$PG{\"blastp\
- gp.pl\"}{\"ADDRESS2\"}=\"http://www.ebi.ac.uk/Tool\
- s/webservices/services/blastpgp\";\n$PG{\"blastpgp\
--.pl\"}{\"language\"}=\"Perl\";\n$PG{\"blastpgp.pl\\
--"}{\"language2\"}=\"Perl\";\n$PG{\"blastpgp.pl\"}{\
--\"source\"}=\"empty\";\n$PG{\"blastpgp.pl\"}{\"upd\
--ate_action\"}=\"never\";\n$PG{\"blastpgp.pl\"}{\"m\
-+.pl\"}{\"language\"}=\"Perl\";\n$PG{\"blastpgp\\
-+"}{\"language2\"}=\"Perl\";\n$PG{\"blastpgp\"}{\
-+\"source\"}=\"empty\";\n$PG{\"blastpgp\"}{\"upd\
-+ate_action\"}=\"never\";\n$PG{\"blastpgp\"}{\"m\
- ode\"}=\"psicoffee,expresso,accurate\";\n$PG{\"bla\
- stcl3\"}{\"4_TCOFFEE\"}=\"NCBIWEBBLAST\";\n$PG{\"b\
- lastcl3\"}{\"type\"}=\"protein_homology_predictor\\
-@@ -5599,15 +5599,15 @@ ables/LATEST\";\n$PG{\"blastall\"}{\"lan
- G{\"blastall\"}{\"source\"}=\"empty\";\n$PG{\"blas\
- tall\"}{\"update_action\"}=\"never\";\n$PG{\"blast\
- all\"}{\"mode\"}=\"psicoffee,expresso,3dcoffee\";\\
--n$PG{\"legacy_blast.pl\"}{\"4_TCOFFEE\"}=\"NCBIBLA\
--ST\";\n$PG{\"legacy_blast.pl\"}{\"type\"}=\"protei\
--n_homology_predictor\";\n$PG{\"legacy_blast.pl\"}{\
-+n$PG{\"legacy_blast\"}{\"4_TCOFFEE\"}=\"NCBIBLA\
-+ST\";\n$PG{\"legacy_blast\"}{\"type\"}=\"protei\
-+n_homology_predictor\";\n$PG{\"legacy_blast\"}{\
- \"ADDRESS\"}=\"ftp://ftp.ncbi.nih.gov/blast/execut\
--ables/LATEST\";\n$PG{\"legacy_blast.pl\"}{\"langua\
--ge\"}=\"C\";\n$PG{\"legacy_blast.pl\"}{\"language2\
--\"}=\"C\";\n$PG{\"legacy_blast.pl\"}{\"source\"}=\\
--"empty\";\n$PG{\"legacy_blast.pl\"}{\"update_actio\
--n\"}=\"never\";\n$PG{\"legacy_blast.pl\"}{\"mode\"\
-+ables/LATEST\";\n$PG{\"legacy_blast\"}{\"langua\
-+ge\"}=\"C\";\n$PG{\"legacy_blast\"}{\"language2\
-+\"}=\"C\";\n$PG{\"legacy_blast\"}{\"source\"}=\\
-+"empty\";\n$PG{\"legacy_blast\"}{\"update_actio\
-+n\"}=\"never\";\n$PG{\"legacy_blast\"}{\"mode\"\
- }=\"psicoffee,expresso,3dcoffee\";\n$PG{\"SOAP::Li\
- te\"}{\"4_TCOFFEE\"}=\"SOAPLITE\";\n$PG{\"SOAP::Li\
- te\"}{\"type\"}=\"library\";\n$PG{\"SOAP::Lite\"}{\
-@@ -6432,7 +6432,7 @@ sults should be written to\n
- ile is written)\n --trace : : \
- show SOAP messages being interchanged\n\nSynchrono\
- us job:\n\n The results/errors are returned as so\
--on as the job is finished.\n Usage: blastpgp.pl -\
-+on as the job is finished.\n Usage: blastpgp -\
- -email <your at email> [options...] seqfile\n Return\
- s: saves the results to disk\n\nAsynchronous job:\\
- n\n Use this if you want to retrieve the results \
-@@ -6442,7 +6442,7 @@ s recommended when users are submitting\
- obs or large database searches\n Usage: blastpgp.\
- pl --email <your at email> --async [options...] seqFi\
- le\n Returns: jobid\n\n Use the jobid to query f\
--or the status of the job.\n Usage: blastpgp.pl --\
-+or the status of the job.\n Usage: blastpgp --\
- status --jobid <jobId>\n Returns: string indicati\
- ng the status of the job\n DONE - job has finis\
- hed\n RUNNING - job is running\n NOT_FOUND -\
---- a/install
-+++ b/install
-@@ -1795,15 +1795,15 @@ $PG{"wublast.pl"}{"language2"}="Perl";
+--- T-COFFEE_distribution_Version_11.00.8cbe486.orig/install
++++ T-COFFEE_distribution_Version_11.00.8cbe486/install
+@@ -1826,15 +1826,15 @@
$PG{"wublast.pl"}{"source"}="empty";
$PG{"wublast.pl"}{"update_action"}="never";
$PG{"wublast.pl"}{"mode"}="psicoffee,expresso,accurate";
@@ -152,10 +51,10 @@
+$PG{"blastpgp"}{"source"}="empty";
+$PG{"blastpgp"}{"update_action"}="never";
+$PG{"blastpgp"}{"mode"}="psicoffee,expresso,accurate";
- $PG{"blastcl3"}{"4_TCOFFEE"}="NCBIWEBBLAST";
- $PG{"blastcl3"}{"type"}="protein_homology_predictor";
- $PG{"blastcl3"}{"ADDRESS"}="ftp://ftp.ncbi.nih.gov/blast/executables/LATEST";
-@@ -1820,14 +1820,14 @@ $PG{"blastall"}{"language2"}="C";
+ $PG{"blastall"}{"4_TCOFFEE"}="blastall";
+ $PG{"blastall"}{"type"}="protein_homology_predictor";
+ $PG{"blastall"}{"ADDRESS"}="ftp://ftp.ncbi.nih.gov/blast/executables/LATEST";
+@@ -1843,14 +1843,14 @@
$PG{"blastall"}{"source"}="empty";
$PG{"blastall"}{"update_action"}="never";
$PG{"blastall"}{"mode"}="psicoffee,expresso,3dcoffee";
@@ -178,9 +77,137 @@
$PG{"SOAP::Lite"}{"4_TCOFFEE"}="SOAPLITE";
$PG{"SOAP::Lite"}{"type"}="library";
$PG{"SOAP::Lite"}{"ADDRESS"}="http://cpansearch.perl.org/src/MKUTTER/SOAP-Lite-0.710.08/Makefile.PL";
---- a/tclinkdb.txt
-+++ b/tclinkdb.txt
-@@ -292,15 +292,15 @@ PG wublast.pl source empty
+--- T-COFFEE_distribution_Version_11.00.8cbe486.orig/t_coffee_source/perl_header_lib.h
++++ T-COFFEE_distribution_Version_11.00.8cbe486/t_coffee_source/perl_header_lib.h
+@@ -31,7 +31,7 @@
+ _method.tc_method","clustalw_method.tc_method","ex\
+ tract_from_pdb","install.pl","clean_cache.pl","nat\
+ ure_protocol.pl","mocca","dalilite.pl","wublast.pl\
+-","blastpgp.pl","ncbiblast_lwp.pl","wublast_lwp.pl\
++","blastpgp","ncbiblast_lwp.pl","wublast_lwp.pl\
+ ","RNAplfold2tclib.pl","fasta_seq2RNAplfold_templa\
+ tefile.pl","fasta_seq2hmmtop_fasta.pl","fasta_seq2\
+ consan_aln.pl","clustalw_aln2fasta_aln.pl","msf_al\
+@@ -1493,7 +1493,7 @@
+ urn 0;}\n }\n else\n {\n $r=`which $p\
+ 2>/dev/null`;\n if ($r eq \"\"){$r=0;}\n else {$r\
+ =1;}\n\n if ($r==0 && is_blast_package ($p)){retur\
+-n pg_is_installed (\"legacy_blast.pl\");}\n else {\
++n pg_is_installed (\"legacy_blast\");}\n else {\
+ return $r;}\n }\n }\n\nsub is_blast_package\\
+ n {\n my $p=shift;\n if ( $p=~/blastp/){ret\
+ urn 1;}\n elsif ($p=~/blastall/){return 1;}\n \
+@@ -2077,7 +2077,7 @@
+ ) {`mv $outfile.xml $outfile`;}\n }\n el\
+ se\n {\n if ($cl_method eq \"psiblast\"){$c\
+ l_method =\"blastp -j5\";}\n\n $command=\"t_coffe\
+-e -other_pg blastpgp.pl --email $EMAIL $infile -d \
++e -other_pg blastpgp --email $EMAIL $infile -d \
+ $db --outfile $outfile -p $cl_method --mode PSI-Bl\
+ ast>/dev/null 2>$error_log\";\n &safe_system ( $c\
+ ommand);\n\n if (-e \"$outfile.xml\") {`mv $outfi\
+@@ -2130,20 +2130,20 @@
+ R\"};\n $cl_db=\"$x$db\";\n }\n else\n \
+ {\n $cl_db=$db;\n }\n\n ##\n \
+ ## BLAST+ provide different binaries names and CLI\
+- options\n ## Use the 'legacy_blast.pl' to keep c\
++ options\n ## Use the 'legacy_blast' to keep c\
+ ompatibility with old blast commands\n ##\n $pat\
+-h=`which legacy_blast.pl 2>/dev/null`; \n $path=\
++h=`which legacy_blast 2>/dev/null`; \n $path=\
+ `dirname $path`; \n chomp($path);\n if ($meth\
+ od eq \"blastp\")\n {\n &check_configuratio\
+-n(\"legacy_blast.pl\");\n $command=\"legacy_blast\
+-.pl blastpgp --path $path -d $cl_db -i $infile -o \
++n(\"legacy_blast\");\n $command=\"legacy_blast\
++ blastpgp --path $path -d $cl_db -i $infile -o \
+ $outfile -m7 -j1\";\n }\n elsif ($method\
+ eq \"psiblast\")\n {\n &check_configuratio\
+-n(\"legacy_blast.pl\");\n $command=\"legacy_blast\
++n(\"legacy_blast\");\n $command=\"legacy_blast\
+ .pl blastpgp --path $path -d $cl_db -i $infile -o \
+ $outfile -m7 -j5\";\n }\n elsif ($method\
+ eq \"blastn\")\n {\n &check_configuration(\
+-\"legacy_blast.pl\");\n $command=\"legacy_blast.p\
++\"legacy_blast\");\n $command=\"legacy_blast.p\
+ l blastall --path $path -p blastn -d $cl_db -i $in\
+ file -o $outfile -m7 -W6\";\n }\n &safe_\
+ system ($command);\n }\n else\n {\n\n myex\
+@@ -5801,16 +5801,16 @@
+ erl\";\n$PG{\"wublast.pl\"}{\"source\"}=\"empty\";\
+ \n$PG{\"wublast.pl\"}{\"update_action\"}=\"never\"\
+ ;\n$PG{\"wublast.pl\"}{\"mode\"}=\"psicoffee,expre\
+-sso,accurate\";\n$PG{\"blastpgp.pl\"}{\"4_TCOFFEE\\
+-"}=\"EBIBLASTPGPc\";\n$PG{\"blastpgp.pl\"}{\"type\\
++sso,accurate\";\n$PG{\"blastpgp\"}{\"4_TCOFFEE\\
++"}=\"EBIBLASTPGPc\";\n$PG{\"blastpgp\"}{\"type\\
+ "}=\"protein_homology_predictor\";\n$PG{\"blastpgp\
+ .pl\"}{\"ADDRESS\"}=\"built_in\";\n$PG{\"blastpgp.\
+ pl\"}{\"ADDRESS2\"}=\"http://www.ebi.ac.uk/Tools/w\
+-ebservices/services/blastpgp\";\n$PG{\"blastpgp.pl\
+-\"}{\"language\"}=\"Perl\";\n$PG{\"blastpgp.pl\"}{\
+-\"language2\"}=\"Perl\";\n$PG{\"blastpgp.pl\"}{\"s\
+-ource\"}=\"empty\";\n$PG{\"blastpgp.pl\"}{\"update\
+-_action\"}=\"never\";\n$PG{\"blastpgp.pl\"}{\"mode\
++ebservices/services/blastpgp\";\n$PG{\"blastpgp\
++\"}{\"language\"}=\"Perl\";\n$PG{\"blastpgp\"}{\
++\"language2\"}=\"Perl\";\n$PG{\"blastpgp\"}{\"s\
++ource\"}=\"empty\";\n$PG{\"blastpgp\"}{\"update\
++_action\"}=\"never\";\n$PG{\"blastpgp\"}{\"mode\
+ \"}=\"psicoffee,expresso,accurate\";\n$PG{\"blasta\
+ ll\"}{\"4_TCOFFEE\"}=\"blastall\";\n$PG{\"blastall\
+ \"}{\"type\"}=\"protein_homology_predictor\";\n$PG\
+@@ -5820,14 +5820,14 @@
+ 2\"}=\"C\";\n$PG{\"blastall\"}{\"source\"}=\"empty\
+ \";\n$PG{\"blastall\"}{\"update_action\"}=\"never\\
+ ";\n$PG{\"blastall\"}{\"mode\"}=\"psicoffee,expres\
+-so,3dcoffee\";\n$PG{\"legacy_blast.pl\"}{\"4_TCOFF\
+-EE\"}=\"NCBIBLAST\";\n$PG{\"legacy_blast.pl\"}{\"t\
++so,3dcoffee\";\n$PG{\"legacy_blast\"}{\"4_TCOFF\
++EE\"}=\"NCBIBLAST\";\n$PG{\"legacy_blast\"}{\"t\
+ ype\"}=\"protein_homology_predictor\";\n$PG{\"lega\
+ cy_blast.pl\"}{\"ADDRESS\"}=\"ftp://ftp.ncbi.nih.g\
+ ov/blast/executables/LATEST\";\n$PG{\"legacy_blast\
+-.pl\"}{\"language\"}=\"C\";\n$PG{\"legacy_blast.pl\
+-\"}{\"language2\"}=\"C\";\n$PG{\"legacy_blast.pl\"\
+-}{\"source\"}=\"empty\";\n$PG{\"legacy_blast.pl\"}\
++.pl\"}{\"language\"}=\"C\";\n$PG{\"legacy_blast\
++\"}{\"language2\"}=\"C\";\n$PG{\"legacy_blast\"\
++}{\"source\"}=\"empty\";\n$PG{\"legacy_blast\"}\
+ {\"update_action\"}=\"never\";\n$PG{\"legacy_blast\
+ .pl\"}{\"mode\"}=\"psicoffee,expresso,3dcoffee\";\\
+ n$PG{\"SOAP::Lite\"}{\"4_TCOFFEE\"}=\"SOAPLITE\";\\
+@@ -6654,23 +6654,23 @@
+ : : show SOAP messages being interc\
+ hanged\n\nSynchronous job:\n\n The results/errors\
+ are returned as soon as the job is finished.\n U\
+-sage: blastpgp.pl --email <your at email> [options...\
++sage: blastpgp --email <your at email> [options...\
+ ] seqfile\n Returns: saves the results to disk\n\\
+ nAsynchronous job:\n\n Use this if you want to re\
+ trieve the results at a later time. The results\n \
+ are stored for up to 24 hours.\n The asynchronou\
+ s submission mode is recommended when users are su\
+ bmitting\n batch jobs or large database searches\\
+-n Usage: blastpgp.pl --email <your at email> --async\
++n Usage: blastpgp --email <your at email> --async\
+ [options...] seqFile\n Returns: jobid\n\n Use t\
+ he jobid to query for the status of the job.\n Us\
+-age: blastpgp.pl --status --jobid <jobId>\n Retur\
++age: blastpgp --status --jobid <jobId>\n Retur\
+ ns: string indicating the status of the job\n D\
+ ONE - job has finished\n RUNNING - job is runni\
+ ng\n NOT_FOUND - job cannot be found\n ERROR\
+ - the jobs has encountered an error\n\n When don\
+ e, use the jobid to retrieve the results of the jo\
+-b.\n Usage: blastpgp.pl --polljob --jobid <jobId>\
++b.\n Usage: blastpgp --polljob --jobid <jobId>\
+ [--outfile <fileName>]\n Returns: saves the resu\
+ lts to disk\nEOF\n;\n}\n","\n=head1 NAME\n\nncbibl\
+ ast_lwp.pl\n\n=head1 DESCRIPTION\n\nNCBI BLAST (RE\
+--- T-COFFEE_distribution_Version_11.00.8cbe486.orig/tclinkdb.txt
++++ T-COFFEE_distribution_Version_11.00.8cbe486/tclinkdb.txt
+@@ -309,15 +309,15 @@
PG wublast.pl update_action never
PG wublast.pl mode psicoffee,expresso,accurate
@@ -203,9 +230,9 @@
+PG blastpgp update_action never
+PG blastpgp mode psicoffee,expresso,accurate
-
- PG blastcl3 4_TCOFFEE NCBIWEBBLAST
-@@ -321,14 +321,14 @@ PG blastall source empty
+ PG blastall 4_TCOFFEE blastall
+ PG blastall type protein_homology_predictor
+@@ -328,14 +328,14 @@
PG blastall update_action never
PG blastall mode psicoffee,expresso,3dcoffee
@@ -228,9 +255,24 @@
PG SOAP::Lite 4_TCOFFEE SOAPLITE
PG SOAP::Lite type library
---- a/t_coffee_source/util_constraints_list.c
-+++ b/t_coffee_source/util_constraints_list.c
-@@ -6340,7 +6340,7 @@ char *** produce_method_file ( char *met
+--- T-COFFEE_distribution_Version_11.00.8cbe486.orig/t_coffee_source/data_headers/programmes_define.h
++++ T-COFFEE_distribution_Version_11.00.8cbe486/t_coffee_source/data_headers/programmes_define.h
+@@ -120,10 +120,10 @@
+ //#define EBIWUBLASTc_ADDRESS "http://www.ebi.ac.uk/Tools/webservices/services/wublast"
+
+
+-#define EBIBLASTPGPc_4_TCOFFEE "blastpgp.pl"
++#define EBIBLASTPGPc_4_TCOFFEE "blastpgp"
+ #define EBIBLASTPGPc_ADDRESS "built_in"
+
+-#define NCBIBLAST_4_TCOFFEE "legacy_blast.pl"
++#define NCBIBLAST_4_TCOFFEE "legacy_blast"
+ #define NCBIBLAST_ADDRESS "ftp://ftp.ncbi.nih.gov/blast/executables/LATEST"
+
+
+--- T-COFFEE_distribution_Version_11.00.8cbe486.orig/t_coffee_source/util_lib/util_constraints_list.c
++++ T-COFFEE_distribution_Version_11.00.8cbe486/t_coffee_source/util_lib/util_constraints_list.c
+@@ -6666,7 +6666,7 @@
sprintf (list[n][0], "blastpgp_client");
sprintf (list[n][1], "%s", vtmpnam(NULL));
n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
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