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debian/changelog
View file @ ba720c2d
t-coffee (12.00.7fb08c2-5) UNRELEASED; urgency=medium
t-coffee (13.30.0.6a5203f-1) UNRELEASED; urgency=medium
[ Michael R. Crusoe ]
* Team upload.
* Unhide the build flags.
* t-coffee-examples: mark Multi-Arch: foreign
-- Michael R. Crusoe <michael.crusoe@gmail.com> Fri, 15 Feb 2019 06:49:18 -0800
[ Andreas Tille ]
* New upstream version
* debhelper-compat 12
* Standards-Version: 4.4.0
-- Andreas Tille <tille@debian.org> Fri, 02 Aug 2019 15:58:34 +0200
t-coffee (12.00.7fb08c2-4) unstable; urgency=medium
......
debian/control
View file @ ba720c2d
......@@ -4,8 +4,8 @@ Uploaders: Steffen Moeller <moeller@debian.org>,
Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 12~)
Standards-Version: 4.3.0
Build-Depends: debhelper-compat (= 12)
Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/t-coffee
Vcs-Git: https://salsa.debian.org/med-team/t-coffee.git
Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
......
debian/patches/clustalw2.patch
View file @ ba720c2d
......@@ -5,44 +5,9 @@ Description: Executable in clustalw 2.x package is named clustalw
Author: Andreas Tille <tille@debian.org>
Last-Update: Fri, 16 Dec 2016 15:00:58 +0100
--- a/t_coffee_source/perl_header_lib.h
+++ b/t_coffee_source/perl_header_lib.h
@@ -5379,7 +5379,7 @@ po_store(\"./src/$pg\");\n }\n else\n
h_command (\"make $arguments sap\");\n &check_\
cp ($pg, \"$BIN\");\n repo_store($pg);\n }\n\
}\n \n #\n # CLUSTALW2 module\n \
-#\n elsif ($pg eq \"clustalw2\")\n {\n &fl\
+#\n elsif ($pg eq \"clustalw\")\n {\n &fl\
ush_command(\"./configure\");\n &flush_command(\"m\
ake $arguments\");\n &check_cp (\"./src/$pg\", \"$\
BIN\");\n repo_store(\"./src/$pg\");\n }\n\n \
@@ -5732,15 +5732,15 @@ nguage\"}=\"C++\";\n$PG{\"strike\"}{\"la
w.tcoffee.org/Projects/strike/strike_v1.2.tar.bz2\\
";\n$PG{\"strike\"}{\"mode\"}=\"tcoffee,expresso\"\
;\n$PG{\"strike\"}{\"version\"}=\"1.2\";\n$PG{\"cl\
-ustalw2\"}{\"4_TCOFFEE\"}=\"CLUSTALW2\";\n$PG{\"cl\
-ustalw2\"}{\"type\"}=\"sequence_multiple_aligner\"\
-;\n$PG{\"clustalw2\"}{\"ADDRESS\"}=\"http://www.cl\
-ustal.org\";\n$PG{\"clustalw2\"}{\"language\"}=\"C\
-++\";\n$PG{\"clustalw2\"}{\"language2\"}=\"CXX\";\\
-n$PG{\"clustalw2\"}{\"source\"}=\"http://www.clust\
+ustalw\"}{\"4_TCOFFEE\"}=\"CLUSTALW2\";\n$PG{\"cl\
+ustalw\"}{\"type\"}=\"sequence_multiple_aligner\"\
+;\n$PG{\"clustalw\"}{\"ADDRESS\"}=\"http://www.cl\
+ustal.org\";\n$PG{\"clustalw\"}{\"language\"}=\"C\
+++\";\n$PG{\"clustalw\"}{\"language2\"}=\"CXX\";\\
+n$PG{\"clustalw\"}{\"source\"}=\"http://www.clust\
al.org/download/2.0.10/clustalw-2.0.10-src.tar.gz\\
-";\n$PG{\"clustalw2\"}{\"mode\"}=\"mcoffee,rcoffee\
-\";\n$PG{\"clustalw2\"}{\"version\"}=\"2.0.10\";\n\
+";\n$PG{\"clustalw\"}{\"mode\"}=\"mcoffee,rcoffee\
+\";\n$PG{\"clustalw\"}{\"version\"}=\"2.0.10\";\n\
$PG{\"clustalw\"}{\"4_TCOFFEE\"}=\"CLUSTALW\";\n$P\
G{\"clustalw\"}{\"type\"}=\"sequence_multiple_alig\
ner\";\n$PG{\"clustalw\"}{\"ADDRESS\"}=\"http://ww\
--- a/t_coffee_source/util_lib/util_constraints_list.c
+++ b/t_coffee_source/util_lib/util_constraints_list.c
@@ -5887,7 +5887,7 @@ char *** produce_method_file ( char *met
@@ -5886,7 +5886,7 @@ char *** produce_method_file ( char *met
sprintf (list[n][1], "%s", vtmpnam(NULL));
n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
fprintf ( fp, "EXECUTABLE profile_pair\n");
......@@ -51,7 +16,7 @@ Last-Update: Fri, 16 Dec 2016 15:00:58 +0100
fprintf ( fp, "ALN_MODE pairwise\n");
fprintf ( fp, "OUT_MODE fL\n");
fprintf ( fp, "IN_FLAG -profile1=\n");
@@ -6162,7 +6162,7 @@ char *** produce_method_file ( char *met
@@ -6161,7 +6161,7 @@ char *** produce_method_file ( char *met
sprintf (list[n][1], "%s", vtmpnam(NULL));
n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
fprintf ( fp, "DOC: clustalw [%s]\n", CLUSTALW2_ADDRESS);
......@@ -60,7 +25,7 @@ Last-Update: Fri, 16 Dec 2016 15:00:58 +0100
fprintf ( fp, "ALN_MODE pairwise\n");
fprintf ( fp, "OUT_MODE aln\n");
fprintf ( fp, "IN_FLAG %sINFILE=\n",CWF);
@@ -6177,7 +6177,7 @@ char *** produce_method_file ( char *met
@@ -6176,7 +6176,7 @@ char *** produce_method_file ( char *met
sprintf (list[n][1], "%s", vtmpnam(NULL));
n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
fprintf ( fp, "DOC clustalw[%s]\n", CLUSTALW2_ADDRESS);
......@@ -69,7 +34,7 @@ Last-Update: Fri, 16 Dec 2016 15:00:58 +0100
fprintf ( fp, "ALN_MODE multiple\n");
fprintf ( fp, "OUT_MODE aln\n");
fprintf ( fp, "IN_FLAG %sINFILE=\n",CWF);
@@ -6192,7 +6192,7 @@ char *** produce_method_file ( char *met
@@ -6191,7 +6191,7 @@ char *** produce_method_file ( char *met
sprintf (list[n][1], "%s", vtmpnam(NULL));
n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
fprintf ( fp, "DOC: clustalw [%s]\n", CLUSTALW_ADDRESS);
......@@ -78,7 +43,7 @@ Last-Update: Fri, 16 Dec 2016 15:00:58 +0100
fprintf ( fp, "ALN_MODE pairwise\n");
fprintf ( fp, "OUT_MODE aln\n");
fprintf ( fp, "IN_FLAG %sINFILE=\n", CWF);
@@ -6207,7 +6207,7 @@ char *** produce_method_file ( char *met
@@ -6206,7 +6206,7 @@ char *** produce_method_file ( char *met
sprintf (list[n][1], "%s", vtmpnam(NULL));
n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
fprintf ( fp, "DOC clustalw[%s]\n", CLUSTALW_ADDRESS);
......@@ -100,7 +65,7 @@ Last-Update: Fri, 16 Dec 2016 15:00:58 +0100
#define CLUSTALO_ADDRESS "http://www.clustal.org/omega/"
--- a/install
+++ b/install
@@ -799,7 +799,7 @@ sub install_source_package
@@ -849,7 +849,7 @@ sub install_source_package
#
# CLUSTALW2 module
#
......@@ -109,10 +74,10 @@ Last-Update: Fri, 16 Dec 2016 15:00:58 +0100
{
&flush_command("./configure");
&flush_command("make $arguments");
@@ -1565,22 +1565,14 @@ $PG{"strike"}{"language2"}="CXX";
$PG{"strike"}{"source"}="http://www.tcoffee.org/Projects/strike/strike_v1.2.tar.bz2";
@@ -1665,23 +1665,14 @@ $PG{"strike"}{"source"}="http://www.tcof
$PG{"strike"}{"mode"}="tcoffee,expresso";
$PG{"strike"}{"version"}="1.2";
$PG{"strike"}{"binary"}="strike";
-$PG{"clustalw2"}{"4_TCOFFEE"}="CLUSTALW2";
-$PG{"clustalw2"}{"type"}="sequence_multiple_aligner";
-$PG{"clustalw2"}{"ADDRESS"}="http://www.clustal.org";
......@@ -120,6 +85,7 @@ Last-Update: Fri, 16 Dec 2016 15:00:58 +0100
-$PG{"clustalw2"}{"language2"}="CXX";
-$PG{"clustalw2"}{"source"}="http://www.clustal.org/download/2.0.10/clustalw-2.0.10-src.tar.gz";
-$PG{"clustalw2"}{"mode"}="mcoffee,rcoffee";
-$PG{"clustalw2"}{"binary"}="clustalw2";
-$PG{"clustalw2"}{"version"}="2.0.10";
-$PG{"clustalw"}{"4_TCOFFEE"}="CLUSTALW";
+$PG{"clustalw"}{"4_TCOFFEE"}="CLUSTALW2";
......@@ -134,15 +100,15 @@ Last-Update: Fri, 16 Dec 2016 15:00:58 +0100
$PG{"clustalw"}{"mode"}="mcoffee,rcoffee";
-$PG{"clustalw"}{"version"}="1.82";
+$PG{"clustalw"}{"version"}="2.0.10";
$PG{"clustalw"}{"binary"}="clustalw";
$PG{"dialign-t"}{"4_TCOFFEE"}="DIALIGNT";
$PG{"dialign-t"}{"type"}="sequence_multiple_aligner";
$PG{"dialign-t"}{"ADDRESS"}="http://dialign-tx.gobics.de/";
--- a/t_coffee_source/programmes_define.h
+++ b/t_coffee_source/programmes_define.h
@@ -61,7 +61,7 @@
#define STRIKE_source "http://www.tcoffee.org/Projects/strike/strike_v1.2.tar.bz2"
@@ -63,7 +63,7 @@
#define STRIKE_mode "tcoffee,expresso"
#define STRIKE_version "1.2"
#define STRIKE_binary "strike"
-#define CLUSTALW2_4_TCOFFEE "clustalw2"
+#define CLUSTALW2_4_TCOFFEE "clustalw"
#define CLUSTALW2_type "sequence_multiple_aligner"
......@@ -150,9 +116,9 @@ Last-Update: Fri, 16 Dec 2016 15:00:58 +0100
#define CLUSTALW2_language "C++"
--- a/tclinkdb.txt
+++ b/tclinkdb.txt
@@ -26,23 +26,14 @@ PG strike source http://www.tcoffee.org
PG strike mode tcoffee,expresso
PG strike version 1.2
@@ -29,24 +29,14 @@ PG strike version 1.2
PG strike binary strike
-PG clustalw2 4_TCOFFEE CLUSTALW2
-PG clustalw2 type sequence_multiple_aligner
......@@ -161,6 +127,7 @@ Last-Update: Fri, 16 Dec 2016 15:00:58 +0100
-PG clustalw2 language2 CXX
-PG clustalw2 source http://www.clustal.org/download/2.0.10/clustalw-2.0.10-src.tar.gz
-PG clustalw2 mode mcoffee,rcoffee
-PG clustalw2 binary clustalw2
-PG clustalw2 version 2.0.10
-
-PG clustalw 4_TCOFFEE CLUSTALW
......@@ -176,6 +143,6 @@ Last-Update: Fri, 16 Dec 2016 15:00:58 +0100
PG clustalw mode mcoffee,rcoffee
-PG clustalw version 1.82
+PG clustalw version 2.0.10
PG clustalw binary clustalw
PG dialign-t 4_TCOFFEE DIALIGNT
PG dialign-t type sequence_multiple_aligner
debian/patches/fix_tempfile_name_sharing.patch
View file @ ba720c2d
......@@ -7,23 +7,12 @@ different processes do not use the same file.
--- a/t_coffee_source/util_lib/reformat.c
+++ b/t_coffee_source/util_lib/reformat.c
@@ -1524,8 +1524,8 @@
@@ -6200,6 +6200,8 @@ Alignment * read_gotoh_aln ( char *fname
}
}
else if (format && (strm(format, "saga_aln" ) ||strm(format, "clustal_aln")||strm(format, "t_coffee_aln" ) || strm (format, "msf_aln")))
{
- static char*tmp_name1=vtmpnam (NULL);
- static char*tmp_name2=vtmpnam (NULL);
+ char*tmp_name1=vtmpnam (NULL);
+ char*tmp_name2=vtmpnam (NULL);
printf_system ( "seq2name_seq.pl %s > %s",name, tmp_name1);
printf_system ( "nameseq2fasta.pl %s > %s",tmp_name1, tmp_name2);
@@ -1534,6 +1534,8 @@
A=seq2aln (S, A, 0);
//read_aln ( name, A);
+ vfree(tmp_name1);
+ vfree(tmp_name2);
}
else if (format && strm (format, "conc_aln"))A=input_conc_aln (name,NULL);
vfclose (fp);
debian/patches/mayhem.patch
View file @ ba720c2d
......@@ -10,7 +10,7 @@ Description: Fix Mayhem issue
--- a/t_coffee_source/util_lib/util.c
+++ b/t_coffee_source/util_lib/util.c
@@ -5275,7 +5275,8 @@ char *get_home_4_tcoffee ()
@@ -5254,7 +5254,8 @@ char *get_home_4_tcoffee ()
}
else
{
......@@ -20,7 +20,7 @@ Description: Fix Mayhem issue
}
@@ -8726,6 +8727,10 @@ int my_mkdir ( char *dir_in)
@@ -8731,6 +8732,10 @@ int my_mkdir ( char *dir_in)
static char *home = getenv ("HOME");
static mode_t oldmask = umask(0);
int change_umask = 0;
......
debian/patches/ncbi-blast++_has_dropped_pl_extension.patch
View file @ ba720c2d
......@@ -9,7 +9,7 @@ Description: Cope with renaming of scripts in ncbi-blast++
--- a/t_coffee_source/programmes_define.h
+++ b/t_coffee_source/programmes_define.h
@@ -336,7 +336,7 @@
@@ -341,7 +341,7 @@
#define EBIWUBLASTc_source "empty"
#define EBIWUBLASTc_update_action "never"
#define EBIWUBLASTc_mode "psicoffee,expresso,accurate"
......@@ -18,7 +18,7 @@ Description: Cope with renaming of scripts in ncbi-blast++
#define EBIBLASTPGPc_type "protein_homology_predictor"
#define EBIBLASTPGPc_ADDRESS "built_in"
#define EBIBLASTPGPc_ADDRESS2 "http://www.ebi.ac.uk/Tools/webservices/services/blastpgp"
@@ -353,7 +353,7 @@
@@ -358,7 +358,7 @@
#define blastall_source "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-src.tar.gz"
#define blastall_update_action "never"
#define blastall_mode "psicoffee,expresso,3dcoffee"
......@@ -29,7 +29,7 @@ Description: Cope with renaming of scripts in ncbi-blast++
#define NCBIBLAST_language "C"
--- a/install
+++ b/install
@@ -1840,15 +1840,15 @@ $PG{"wublast.pl"}{"language2"}="Perl";
@@ -1943,15 +1943,15 @@ $PG{"wublast.pl"}{"language2"}="Perl";
$PG{"wublast.pl"}{"source"}="empty";
$PG{"wublast.pl"}{"update_action"}="never";
$PG{"wublast.pl"}{"mode"}="psicoffee,expresso,accurate";
......@@ -54,7 +54,7 @@ Description: Cope with renaming of scripts in ncbi-blast++
$PG{"blastall"}{"4_TCOFFEE"}="blastall";
$PG{"blastall"}{"type"}="protein_homology_predictor";
$PG{"blastall"}{"ADDRESS"}="ftp://ftp.ncbi.nih.gov/blast/executables/LATEST";
@@ -1857,14 +1857,14 @@ $PG{"blastall"}{"language2"}="C";
@@ -1960,14 +1960,14 @@ $PG{"blastall"}{"language2"}="C";
$PG{"blastall"}{"source"}="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-src.tar.gz";
$PG{"blastall"}{"update_action"}="never";
$PG{"blastall"}{"mode"}="psicoffee,expresso,3dcoffee";
......@@ -77,82 +77,9 @@ Description: Cope with renaming of scripts in ncbi-blast++
$PG{"SOAP::Lite"}{"4_TCOFFEE"}="SOAPLITE";
$PG{"SOAP::Lite"}{"type"}="library";
$PG{"SOAP::Lite"}{"ADDRESS"}="http://cpansearch.perl.org/src/MKUTTER/SOAP-Lite-0.710.08/Makefile.PL";
--- a/t_coffee_source/perl_header_lib.h
+++ b/t_coffee_source/perl_header_lib.h
@@ -31,7 +31,7 @@ tc_generic_method.pl","rnapdb2protpdb.pl
_method.tc_method","clustalw_method.tc_method","ex\
tract_from_pdb","install.pl","clean_cache.pl","nat\
ure_protocol.pl","mocca","dalilite.pl","wublast.pl\
-","blastpgp.pl","ncbiblast_lwp.pl","wublast_lwp.pl\
+","blastpgp","ncbiblast_lwp.pl","wublast_lwp.pl\
","RNAplfold2tclib.pl","fasta_seq2RNAplfold_templa\
tefile.pl","fasta_seq2hmmtop_fasta.pl","fasta_seq2\
consan_aln.pl","clustalw_aln2fasta_aln.pl","seq2na\
@@ -1558,7 +1558,7 @@ rl -M$p -e 1\")==$EXIT_SUCCESS){return 1
{return 0;}\n }\n else\n {\n $r=`whic\
h $p 2>/dev/null`;\n if ($r eq \"\"){$r=0;}\n else\
{$r=1;}\n\n if ($r==0 && is_blast_package ($p)){r\
-eturn pg_is_installed (\"legacy_blast.pl\");}\n el\
+eturn pg_is_installed (\"legacy_blast\");}\n el\
se {return $r;}\n }\n }\n\nsub is_blast_pack\
age\n {\n my $p=shift;\n if ( $p=~/blastp/)\
{return 1;}\n elsif ($p=~/blastall/){return 1;}\
@@ -2230,19 +2230,19 @@ L\")\n {\n if ($ENV{\"BLAST_DB_DIR
n ##\n ## BLAST+ provide different binarie\
s names and CLI options\n ## Use the 'legacy_blas\
t.pl' to keep compatibility with old blast command\
-s\n ##\n $path=`which legacy_blast.pl 2>/dev/nul\
+s\n ##\n $path=`which legacy_blast 2>/dev/nul\
l`; \n $path=`dirname $path`; \n chomp($path);\\
n if ($method eq \"blastp\"){\n &check_confi\
-guration(\"legacy_blast.pl\");\n $command=\"lega\
-cy_blast.pl blastpgp --path $path -d $cl_db -i $in\
+guration(\"legacy_blast\");\n $command=\"lega\
+cy_blast blastpgp --path $path -d $cl_db -i $in\
file -o $outfile -m7 -j1\";\n }\n elsif ($\
method eq \"psiblast\")\n {\n &check_config\
-uration(\"legacy_blast.pl\");\n $command=\"legacy\
-_blast.pl blastpgp --path $path -d $cl_db -i $infi\
+uration(\"legacy_blast\");\n $command=\"legacy\
+_blast blastpgp --path $path -d $cl_db -i $infi\
le -o $outfile -m7 -j5\";\n }\n elsif ($\
method eq \"blastn\")\n {\n &check_configur\
-ation(\"legacy_blast.pl\");\n $command=\"legacy_b\
-last.pl blastall --path $path -p blastn -d $cl_db \
+ation(\"legacy_blast\");\n $command=\"legacy_b\
+last blastall --path $path -p blastn -d $cl_db \
-i $infile -o $outfile -m7 -W6\";\n }\n \
&safe_system ($command);\n }\n else\n {\n\n \
myexit(add_error (EXIT_FAILURE,$$,$$,getppid(), \
@@ -6046,17 +6046,17 @@ tp.ncbi.nlm.nih.gov/blast/executables/bl
/ncbi-blast-2.6.0+-src.tar.gz\";\n$PG{\"blastall\"\
}{\"update_action\"}=\"never\";\n$PG{\"blastall\"}\
{\"mode\"}=\"psicoffee,expresso,3dcoffee\";\n$PG{\\
-"legacy_blast.pl\"}{\"4_TCOFFEE\"}=\"NCBIBLAST\";\\
-n$PG{\"legacy_blast.pl\"}{\"type\"}=\"protein_homo\
-logy_predictor\";\n$PG{\"legacy_blast.pl\"}{\"ADDR\
+"legacy_blast\"}{\"4_TCOFFEE\"}=\"NCBIBLAST\";\\
+n$PG{\"legacy_blast\"}{\"type\"}=\"protein_homo\
+logy_predictor\";\n$PG{\"legacy_blast\"}{\"ADDR\
ESS\"}=\"ftp://ftp.ncbi.nih.gov/blast/executables/\
-LATEST\";\n$PG{\"legacy_blast.pl\"}{\"language\"}=\
-\"C\";\n$PG{\"legacy_blast.pl\"}{\"language2\"}=\"\
-C\";\n$PG{\"legacy_blast.pl\"}{\"source\"}=\"ftp:/\
+LATEST\";\n$PG{\"legacy_blast\"}{\"language\"}=\
+\"C\";\n$PG{\"legacy_blast\"}{\"language2\"}=\"\
+C\";\n$PG{\"legacy_blast\"}{\"source\"}=\"ftp:/\
/ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6\
.0/ncbi-blast-2.6.0+-src.tar.gz\";\n$PG{\"legacy_b\
-last.pl\"}{\"update_action\"}=\"never\";\n$PG{\"le\
-gacy_blast.pl\"}{\"mode\"}=\"psicoffee,expresso,3d\
+last\"}{\"update_action\"}=\"never\";\n$PG{\"le\
+gacy_blast\"}{\"mode\"}=\"psicoffee,expresso,3d\
coffee\";\n$PG{\"SOAP::Lite\"}{\"4_TCOFFEE\"}=\"SO\
APLITE\";\n$PG{\"SOAP::Lite\"}{\"type\"}=\"library\
\";\n$PG{\"SOAP::Lite\"}{\"ADDRESS\"}=\"http://cpa\
--- a/tclinkdb.txt
+++ b/tclinkdb.txt
@@ -340,15 +340,15 @@ PG wublast.pl source empty
@@ -346,15 +346,15 @@ PG wublast.pl source empty
PG wublast.pl update_action never
PG wublast.pl mode psicoffee,expresso,accurate
......@@ -177,7 +104,7 @@ Description: Cope with renaming of scripts in ncbi-blast++
PG blastall 4_TCOFFEE blastall
PG blastall type protein_homology_predictor
@@ -359,14 +359,14 @@ PG blastall source ftp://ftp.ncbi.nlm.n
@@ -365,14 +365,14 @@ PG blastall source ftp://ftp.ncbi.nlm.n
PG blastall update_action never
PG blastall mode psicoffee,expresso,3dcoffee
......@@ -217,7 +144,7 @@ Description: Cope with renaming of scripts in ncbi-blast++
--- a/t_coffee_source/util_lib/util_constraints_list.c
+++ b/t_coffee_source/util_lib/util_constraints_list.c
@@ -7459,7 +7459,7 @@ char *** produce_method_file ( char *met
@@ -7458,7 +7458,7 @@ char *** produce_method_file ( char *met
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");
......@@ -226,3 +153,151 @@ Description: Cope with renaming of scripts in ncbi-blast++
fprintf ( fp, "ALN_MODE predict\n");
fprintf ( fp, "SEQ_TYPE PROTEIN\n");
--- a/t_coffee_source/perl_header_lib.h
+++ b/t_coffee_source/perl_header_lib.h
@@ -30,7 +30,7 @@ msa2bootstrap.pl","tc_generic_method.pl"
rotpdb.pl","generic_method.tc_method","clustalw_me\
thod.tc_method","extract_from_pdb","install.pl","c\
lean_cache.pl","nature_protocol.pl","mocca","dalil\
-ite.pl","wublast.pl","blastpgp.pl","ncbiblast_lwp.\
+ite.pl","wublast.pl","blastpgp","ncbiblast_lwp.\
pl","wublast_lwp.pl","RNAplfold2tclib.pl","fasta_s\
eq2RNAplfold_templatefile.pl","fasta_seq2hmmtop_fa\
sta.pl","fasta_seq2consan_aln.pl","clustalw_aln2fa\
@@ -1789,7 +1789,7 @@ fe_system ( $command);\n if (-e \"$outf
{`mv $outfile.xml $outfile`;}\n }\n els\
e\n {\n if ($cl_method eq \"psiblast\"){$cl\
_method =\"blastp -j5\";}\n\n $command=\"t_coffee\
- -other_pg blastpgp.pl --email $EMAIL $infile -d $\
+ -other_pg blastpgp --email $EMAIL $infile -d $\
db --outfile $outfile -p $cl_method --mode PSI-Bla\
st>/dev/null 2>$error_log\";\n &safe_system ( $co\
mmand);\n\n if (-e \"$outfile.xml\") {`mv $outfil\
@@ -1861,20 +1861,20 @@ LAST_DB_DIR\"}) {\n $x=$ENV{\"BLAST
;\n $cl_db=\"$x/$db\";\n }\n else{\n $\
cl_db=$db;\n }\n\n ##\n ## BLAST+ prov\
ide different binaries names and CLI options\n ##\
- Use the 'legacy_blast.pl' to keep compatibility w\
+ Use the 'legacy_blast' to keep compatibility w\
ith old blast commands\n ##\n $path=`which legac\
y_blast.pl 2>/dev/null`; \n $path=`dirname $path\
`; \n chomp($path);\n if ($method eq \"blastp\
-\"){\n &check_configuration(\"legacy_blast.pl\")\
-;\n $command=\"legacy_blast.pl blastpgp --path $\
+\"){\n &check_configuration(\"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_configuration(\"legacy_blast.pl\");\
-\n $command=\"legacy_blast.pl blastpgp --path $pa\
+ {\n &check_configuration(\"legacy_blast\");\
+\n $command=\"legacy_blast blastpgp --path $pa\
th -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.pl blastall --path $path\
+ {\n &check_configuration(\"legacy_blast\");\n\
+ $command=\"legacy_blast blastall --path $path\
-p blastn -d $cl_db -i $infile -o $outfile -m7 -W\
6\";\n }\n &safe_system ($command);\n \
}\n else\n {\n\n myexit(add_error (EXIT_FAIL\
@@ -5042,7 +5042,7 @@ istribution\n `rm *.o sap sap.exe .
"make $arguments sap\");\n &check_cp ($pg, \"$\
BIN\");\n repo_store($pg);\n }\n }\n \
\n #\n # CLUSTALW2 module\n #\n elsif\
- ($pg eq \"clustalw2\")\n {\n &flush_command(\
+ ($pg eq \"clustalw\")\n {\n &flush_command(\
\"./configure\");\n &flush_command(\"make $argumen\
ts\");\n &check_cp (\"./src/$pg\", \"$BIN\");\n re\
po_store(\"./src/$pg\");\n }\n\n #\n # \
@@ -5419,16 +5419,16 @@ DDRESS\"}=\"http://www.tcoffee.org/Proje
Projects/strike/strike_v1.2.tar.bz2\";\n$PG{\"stri\
ke\"}{\"mode\"}=\"tcoffee,expresso\";\n$PG{\"strik\
e\"}{\"version\"}=\"1.2\";\n$PG{\"strike\"}{\"bina\
-ry\"}=\"strike\";\n$PG{\"clustalw2\"}{\"4_TCOFFEE\\
-"}=\"CLUSTALW2\";\n$PG{\"clustalw2\"}{\"type\"}=\"\
-sequence_multiple_aligner\";\n$PG{\"clustalw2\"}{\\
+ry\"}=\"strike\";\n$PG{\"clustalw\"}{\"4_TCOFFEE\\
+"}=\"CLUSTALW2\";\n$PG{\"clustalw\"}{\"type\"}=\"\
+sequence_multiple_aligner\";\n$PG{\"clustalw\"}{\\
"ADDRESS\"}=\"http://www.clustal.org\";\n$PG{\"clu\
-stalw2\"}{\"language\"}=\"C++\";\n$PG{\"clustalw2\\
-"}{\"language2\"}=\"CXX\";\n$PG{\"clustalw2\"}{\"s\
+stalw2\"}{\"language\"}=\"C++\";\n$PG{\"clustalw\\
+"}{\"language2\"}=\"CXX\";\n$PG{\"clustalw\"}{\"s\
ource\"}=\"http://www.clustal.org/download/2.0.10/\
-clustalw-2.0.10-src.tar.gz\";\n$PG{\"clustalw2\"}{\
-\"mode\"}=\"mcoffee,rcoffee\";\n$PG{\"clustalw2\"}\
-{\"binary\"}=\"clustalw2\";\n$PG{\"clustalw2\"}{\"\
+clustalw-2.0.10-src.tar.gz\";\n$PG{\"clustalw\"}{\
+\"mode\"}=\"mcoffee,rcoffee\";\n$PG{\"clustalw\"}\
+{\"binary\"}=\"clustalw\";\n$PG{\"clustalw\"}{\"\
version\"}=\"2.0.10\";\n$PG{\"clustalw\"}{\"4_TCOF\
FEE\"}=\"CLUSTALW\";\n$PG{\"clustalw\"}{\"type\"}=\
\"sequence_multiple_aligner\";\n$PG{\"clustalw\"}{\
@@ -5715,16 +5715,16 @@ e\"}=\"Perl\";\n$PG{\"wublast.pl\"}{\"la
=\"Perl\";\n$PG{\"wublast.pl\"}{\"source\"}=\"empt\
y\";\n$PG{\"wublast.pl\"}{\"update_action\"}=\"nev\
er\";\n$PG{\"wublast.pl\"}{\"mode\"}=\"psicoffee,e\
-xpresso,accurate\";\n$PG{\"blastpgp.pl\"}{\"4_TCOF\
-FEE\"}=\"EBIBLASTPGPc\";\n$PG{\"blastpgp.pl\"}{\"t\
+xpresso,accurate\";\n$PG{\"blastpgp\"}{\"4_TCOF\
+FEE\"}=\"EBIBLASTPGPc\";\n$PG{\"blastpgp\"}{\"t\
ype\"}=\"protein_homology_predictor\";\n$PG{\"blas\
tpgp.pl\"}{\"ADDRESS\"}=\"built_in\";\n$PG{\"blast\
pgp.pl\"}{\"ADDRESS2\"}=\"http://www.ebi.ac.uk/Too\
ls/webservices/services/blastpgp\";\n$PG{\"blastpg\
-p.pl\"}{\"language\"}=\"Perl\";\n$PG{\"blastpgp.pl\
-\"}{\"language2\"}=\"Perl\";\n$PG{\"blastpgp.pl\"}\
-{\"source\"}=\"empty\";\n$PG{\"blastpgp.pl\"}{\"up\
-date_action\"}=\"never\";\n$PG{\"blastpgp.pl\"}{\"\
+p.pl\"}{\"language\"}=\"Perl\";\n$PG{\"blastpgp\
+\"}{\"language2\"}=\"Perl\";\n$PG{\"blastpgp\"}\
+{\"source\"}=\"empty\";\n$PG{\"blastpgp\"}{\"up\
+date_action\"}=\"never\";\n$PG{\"blastpgp\"}{\"\
mode\"}=\"psicoffee,expresso,accurate\";\n$PG{\"bl\
astall\"}{\"4_TCOFFEE\"}=\"blastall\";\n$PG{\"blas\
tall\"}{\"type\"}=\"protein_homology_predictor\";\\
@@ -5736,17 +5736,17 @@ tp://ftp.ncbi.nlm.nih.gov/blast/executab
/2.6.0/ncbi-blast-2.6.0+-src.tar.gz\";\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$PG{\"legacy_blast.pl\"}{\"source\"}=\\
+ables/LATEST\";\n$PG{\"legacy_blast\"}{\"langua\
+ge\"}=\"C\";\n$PG{\"legacy_blast\"}{\"language2\
+\"}=\"C\";\n$PG{\"legacy_blast\"}{\"source\"}=\\
"ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blas\
t+/2.6.0/ncbi-blast-2.6.0+-src.tar.gz\";\n$PG{\"le\
gacy_blast.pl\"}{\"update_action\"}=\"never\";\n$P\
-G{\"legacy_blast.pl\"}{\"mode\"}=\"psicoffee,expre\
+G{\"legacy_blast\"}{\"mode\"}=\"psicoffee,expre\
sso,3dcoffee\";\n$PG{\"SOAP::Lite\"}{\"4_TCOFFEE\"\
}=\"SOAPLITE\";\n$PG{\"SOAP::Lite\"}{\"type\"}=\"l\
ibrary\";\n$PG{\"SOAP::Lite\"}{\"ADDRESS\"}=\"http\
@@ -6596,7 +6596,7 @@ results should be written to\n
file is written)\n --trace : \
: show SOAP messages being interchanged\n\nSynchro\
nous job:\n\n The results/errors are returned as \
-soon as the job is finished.\n Usage: blastpgp.pl\
+soon as the job is finished.\n Usage: blastpgp\
--email <your@email> [options...] seqfile\n Retu\
rns: saves the results to disk\n\nAsynchronous job\
:\n\n Use this if you want to retrieve the result\
@@ -6606,7 +6606,7 @@ p to 24 hours.\n The asynchronous submi
jobs or large database searches\n Usage: blastpg\
p.pl --email <your@email> --async [options...] seq\
File\n Returns: jobid\n\n Use the jobid to query\
- for the status of the job.\n Usage: blastpgp.pl \
+ for the status of the job.\n Usage: blastpgp \
--status --jobid <jobId>\n Returns: string indica\
ting the status of the job\n DONE - job has fin\
ished\n RUNNING - job is running\n NOT_FOUND\
debian/patches/set_proper_dir_permissions.patch
View file @ ba720c2d
......@@ -6,7 +6,7 @@ Description: When creating subdirectories in $HOME do not
--- a/t_coffee_source/util_lib/util.c
+++ b/t_coffee_source/util_lib/util.c
@@ -8723,6 +8723,10 @@ int my_mkdir ( char *dir_in)
@@ -8728,6 +8728,10 @@ int my_mkdir ( char *dir_in)
int a, buf;
char *dir;
......@@ -17,7 +17,7 @@ Description: When creating subdirectories in $HOME do not
dir=(char*)vcalloc ( strlen (dir_in)+strlen (get_home_4_tcoffee())+100, sizeof (char));
sprintf ( dir, "%s", dir_in);
@@ -8742,10 +8746,11 @@ int my_mkdir ( char *dir_in)
@@ -8747,10 +8751,11 @@ int my_mkdir ( char *dir_in)
if (access(dir, F_OK)==-1)
{
......
install
View file @ ba720c2d
......@@ -9,7 +9,11 @@ use strict;
our (%MODE, %PG, %ENV_SET, %SUPPORTED_OS);
#DO NOT EDIT MANUALLY START
#To be populated with edit_version.pl
our $VERSION="0";
our $VERSION="Version_13.30.0.6a5203f";#POPULATED by edit_version.pl from #_#UPDATE_VERSION
#DO NOT EDIT MANUALLY END
our $EXIT_SUCCESS=0;
our $EXIT_FAILURE=1;
our $INTERNET=0;
......@@ -37,6 +41,8 @@ our $TCMETHODS;
our $TCPLUGINS;
our $PLUGINS_DIR="";
our $INSTALL_DIR="";
our $email;
our $recompile;
########### DEFINITIONS ##############################
#
......@@ -64,7 +70,6 @@ my @smode=("all", "clean", "install");
########################################################
&initialize_PG();
#Parse The Command Line
my $cl=join( " ", @ARGV);
if ($#ARGV==-1 || ($cl=~/-h/) ||($cl=~/-H/) )
......@@ -88,6 +93,8 @@ if (($cl=~/-h/) ||($cl=~/-H/) )
print "!!!!!!! ./install [target:package|mode|] [-update|-force|-exec=dir|-dis=dir|-root|-tclinkdb=file|-] [CC=|FCC=|CXX=|CFLAGS=|CXXFLAGS=]\n";
print "!!!!!!! ./install clean [removes all executables]\n";
print "!!!!!!! ./install [optional:target] -update [updates package already installed]\n";
print "!!!!!!! ./install [optional:target] -recompile [forces the recompilation of T-Coffee]\n";
print "!!!!!!! ./install [optional:target] -force [Forces recompilation over everything]\n";
print "!!!!!!! ./install [optional:target] -root [You are running as root]\n";
......@@ -96,8 +103,11 @@ if (($cl=~/-h/) ||($cl=~/-H/) )
print "!!!!!!! ./install [optional:target] -tclinkdb=foo|update [file containing all the packages to be installed]\n";
print "!!!!!!! ./install [optional:target] -clean [clean everything]\n";
print "!!!!!!! ./install [optional:target] -plugins [plugins directory]\n";
print "!!!!!!! ./install [optional:target] -tcdir=/foor/bar [base path where T-Coffee will be installed]\n";
print "!!!!!!! ./install [optional:target] -tcdir=/foor/bar [base path where T-Coffee will be installed - default ~/.t_coffee]\n";
print "!!!!!!! ./install [optional:target] -repo=/path/to/repo [binaries repository root directory]\n";
print "!!!!!!! ./install [optional:target] -email=<your email> [needed for remote BLAST]\n";
print "!!!!!!! ./install [optional:target] -proxy=<proxy> [may be needed to access remote services]\n";
print "!!!!!!! mode:";
foreach $m (keys(%MODE)){print "$m ";}
print "\n";
......@@ -128,7 +138,12 @@ our ($ROOT_INSTALL, $NO_QUESTION, $default_update_action,$BINARIES_ONLY,$force,
if ( ($cl=~/-root/)){$ROOT_INSTALL=1;}
if ( ($cl=~/-no_question/)){$NO_QUESTION=1;}
if ( ($cl=~/-update/)){$default_update_action="update";}
if ( ($cl=~/-recompile/)){$recompile=1;}
#By defualt the program will attempt to install packages from binaries maintained on www.tcoffee.org
$BINARIES_ONLY=1;
if ( ($cl=~/-nobinaries/)){$BINARIES_ONLY=0;}
if ( ($cl=~/-force/)){$force=1;$default_update_action="update"}
if ( ($cl=~/-exec=\s*(\S+)/)){$INSTALL_DIR=$1;}
......@@ -140,6 +155,10 @@ if ( ($cl=~/-proxy=\s*(\S+)/)){$proxy=$1;}
if ( ($cl=~/-clean/)){$clean=1;}
if ( ($cl=~/-repo=\s*(\S+)/)){ $REPO_ROOT=$1; }
if ( ($cl=~/-tcdir=\s*(\S+)/)){ $TCDIR=$1; }
if ( ($cl=~/-email=\s*(\S+)/)){$email=$1;}
#automated update
if ($tclinkdb){&update_tclinkdb ($tclinkdb);}
......@@ -162,10 +181,10 @@ if(!$TCDIR) { $TCDIR="$HOME/.t_coffee"; }
#Prepare the Installation Structure
our $BASE="$CD/bin";
our $BIN="$BASE/binaries/$OS";
our $DOWNLOAD_DIR="$BASE/download";
our $BIN="$BASE/cache/binaries/$OS";
our $DOWNLOAD_DIR="$BASE/cache/download";
our $DOWNLOAD_FILE="$DOWNLOAD_DIR/files";
our $TMP="$BASE/tmp";
our $TMP="$BASE/cache/tmp";
&add_dir($BASE);
&add_dir($BIN);
......@@ -181,7 +200,7 @@ if (!$PLUGINS_DIR && !$ROOT_INSTALL){$PLUGINS_DIR=$TCPLUGINS;}
elsif (!$PLUGINS_DIR && $ROOT_INSTALL){$PLUGINS_DIR="/usr/local/bin/";}
#set the directory for t_coffee
if (!$INSTALL_DIR && !$ROOT_INSTALL){$INSTALL_DIR="$HOME/bin/";mkpath ($INSTALL_DIR);}
if (!$INSTALL_DIR && !$ROOT_INSTALL){$INSTALL_DIR="$TCDIR/bin/$OS";mkpath ($INSTALL_DIR);}
elsif (!$INSTALL_DIR && $ROOT_INSTALL){$INSTALL_DIR="/usr/local/bin/";}
#prepare mcoffee files [Only if vanilla installation]
......@@ -189,9 +208,15 @@ if (-d "mcoffee"){`cp mcoffee/* $TCM`;}
#prepare the environement
our $ENV_FILE="$TCDIR/t_coffee_env";
our $ENV_FILE="$TCDIR/.t_coffee_env";
unlink ($ENV_FILE);
&add2env_file ($ENV_FILE,"EMAIL_4_TCOFFEE", $email);
&add2env_file ($ENV_FILE,"http_proxy_4_TCOFFEE", $proxy);
&env_file2putenv ($ENV_FILE);
&set_proxy($proxy);
my ($target, $p, $r);
$target=$p;
......@@ -395,12 +420,21 @@ if ($failure)
print "*********************************************************************\n";
print "******** FINALIZE YOUR INSTALLATION *****************\n";
print "*********************************************************************\n";
print "------- Your executables are in:\n";
print "------- Your third party executables are in:\n";
print "------- $PLUGINS_DIR:\n";
print "------- Add this directory to your path with the following command:\n";
print "------- export PATH=$PLUGINS_DIR:\$PATH\n";
print "------- Make this permanent by adding this line to the file:\n";
print "------- $HOME/.bashrc\n";
print "------- Your t_coffee exccutable is in\n";
print "------- $INSTALL_DIR:\n";
print "------- In order to make your installation permanent add these two lines\n";
print "------- export PATH=$INSTALL_DIR:\$PATH\n";
print "------- export PLUGINS_4_TCOFFEE=$PLUGINS_DIR:\n";
if ($OS eq "linux")
{
print "------- to the file: $HOME/.bashrc\n";
}
else
{
print "------- to the file: $HOME/.profile\n";
}
exit ($EXIT_SUCCESS);
#################################################################################
......@@ -506,7 +540,7 @@ sub url2file
exit ($EXIT_FAILURE);
}
if (&pg_is_installed ("wget")){$pg="wget"; $flag="-O";$arg="--tries=2 --connect-timeout=10 $wget_arg";}
if (&pg_is_installed ("wget")){$pg="wget"; $flag="-O";$arg="--tries=2 --connect-timeout=10 --no-check-certificate $wget_arg";}
elsif (&pg_is_installed ("curl")){$pg="curl"; $flag="-o";$arg=$curl_arg;}
else
{
......@@ -561,14 +595,22 @@ sub install
if (!$ROOT_INSTALL)
{
if (-e "$BIN/t_coffee"){`$CP $BIN/t_coffee $INSTALL_DIR`};
`cp $BIN/* $PLUGINS_DIR`;
`$CP $BIN/* $PLUGINS_DIR`;
if (-e "$BIN/t_coffee")
{
`$CP $BIN/t_coffee $INSTALL_DIR`;
unlink("$PLUGINS_DIR/t_coffee");
}
$copied=1;
}
else
{
$copied=&root_run ("You must be root to finalize the installation", "$CP $BIN/* $INSTALL_DIR $SILENT");
$copied=&root_run ("You must be root to finalize the installation", "$CP $BIN/* $PLUGINS_DIR $SILENT");
if (-e "$BIN/t_coffee")
{
&root_run ("You must be root to finalize the installation", "$CP $BIN/t_coffee $INSTALL_DIR");
&root_run ("You must be root to finalize the installation", "rm $PLUGINS_DIR/t_coffee");
}
}
......@@ -582,10 +624,18 @@ sub install
}
elsif ( $copied && !$ROOT)
{
$report= "*!!!!!! T-Coffee and associated packages have been copied in: $new_bin\n";
$report.="*!!!!!! This address is NOT in your PATH sytem variable\n";
$report= "*!!!!!! T-Coffee has been installed in $INSTALL_DIR\n";
$report= "*!!!!!! T-Coffee and associated packages have been copied in: $PLUGINS_DIR\n";
$report.="*!!!!!! This T-Coffee location is NOT on your PATH sytem variable\n";
if ( $OS eq "linux")
{
$report.="*!!!!!! You can do so by adding the following line in your ~/.bashrc file:\n";
$report.="*!!!!!! export PATH=$new_bin:\$PATH\n";
}
else
{
$report.="*!!!!!! You can do so by adding the following line in your ~/.profile file:\n";
}
$report.="*!!!!!! export PATH=$INSTALL_DIR:\$PATH\n";
}
return $report;
}
......@@ -606,7 +656,7 @@ sub sign_license_ni
# #
# #
# #
# INDIVIDUAL MULTIPLE SEQUENCE ALIGNMNT PACKAGES INSTALLATION #
# INDIVIDUAL MULTIPLE SEQUENCE ALIGNMENT PACKAGES INSTALLATION #
# #
# #
# #
......@@ -632,7 +682,7 @@ sub install_pg
$PG{$pg}{old}=$previous;
if ($PG{$pg} {language2} eq "Perl"){&install_perl_package ($pg);}
elsif ($pg ne "t_coffee" && $BINARIES_ONLY && &install_binary_package ($pg)){$PG{$pg}{from_binary}=1;}
elsif ($BINARIES_ONLY && &install_binary_package ($pg)){$PG{$pg}{from_binary}=1;}
elsif (&install_source_package ($pg)){;}
else
{
......@@ -677,7 +727,7 @@ sub install_source_package
my ($report, $download, $arguments, $language, $address, $name, $ext, $main_dir, $distrib);
my $wget_tmp="$TMP/wget.tmp";
my (@fl);
if ( -e "$BIN/$pg" || -e "$BIN/$pg.exe"){return 1;}
if ( $default_update_action ne "update" && (-e "$BIN/$pg" || -e "$BIN/$pg.exe" ) ){return 1;}
#
# check if the module exists in the repository cache
......@@ -686,7 +736,7 @@ sub install_source_package
return 1;
}
if ($pg eq "t_coffee") {return &install_t_coffee ($pg);}
if ($pg eq "t_coffee") {return &install_t_coffee_source ($pg);}
elsif ($pg eq "TMalign"){return &install_TMalign ($pg);}
chdir $DISTRIBUTIONS;
......@@ -742,7 +792,7 @@ sub install_source_package
print "\n------- unzipping/untaring $name\n";
if (($ext =~/z/))
{
&flush_command ("gunzip $name$ext");
&flush_command ("gunzip -f $name$ext");
}
if (($ext =~/tar/) || ($ext =~/tgz/))
......@@ -1105,10 +1155,11 @@ sub install_source_package
return &pg_is_installed ($pg, $BIN);
}
sub install_t_coffee
sub install_t_coffee_source
{
my ($pg)=(@_);
my ($report,$cflags, $arguments, $language, $compiler) ;
#1-Install T-Coffee
chdir "t_coffee_source";
&flush_command ("make clean");
......@@ -1116,7 +1167,8 @@ sub install_t_coffee
$language=$PG{$pg} {language2};
$arguments=$PG{$language}{arguments};
if ( $CC ne ""){
if ( $CC ne "")
{
print "make -i $arguments t_coffee \n";
&flush_command ("make -i $arguments t_coffee");
}
......@@ -1150,6 +1202,8 @@ sub pg_has_binary_distrib
my ($pg)=(@_);
if ($PG{$pg}{windows}){return 1;}
elsif ($PG{$pg}{osx}){return 1;}
elsif ($PG{$pg}{macosx}){return 1;}
elsif ($PG{$pg}{linux}){return 1;}
return 0;
}
......@@ -1172,8 +1226,26 @@ sub install_binary_package
if (!&supported_os($OS)){return 0;}
if ( $PG{$pg}{binary}){$name=$PG{$pg}{binary};}
else {$name=$pg;}
$download="$WEB_BASE/Packages/Binaries/$OS/$name";
if ($name eq "t_coffee")
{
#check if local bin is there
if (-e "./bin/$OS/t_coffee")
{
print "\n------- Installing T-Coffee from Pre-Compiled/Pre-Downloaded $OS binary\n";
print "\n------- If you want to trigger a fresh compilation use -recompile\n";
&check_cp ("./bin/$OS/t_coffee", $BIN);
return &pg_is_installed ($pg, $BIN);
}
#try to get precompiled binary -- available from MAC is distribution from MAC
else
{
$download="$WEB_BASE/Packages/Binaries/tcoffee/$OS/$name.$VERSION";
}
}
else
{
$download="$WEB_BASE/Packages/Binaries/plugins/$OS/$name";
}
$base=cwd();
chdir $TMP;
......@@ -1191,13 +1263,14 @@ sub install_binary_package
{
print "!!!!!!! $PG{$pg}{dname}: Download of $pg binary failed\n";
print "!!!!!!! $PG{$pg}{dname}: Check Address: $download\n";
chdir $base;
return 0;
}
print "\n------- Installing $pg\n";
if ($name =~/tar\.gz/)
{
`gunzip $name`;
`gunzip -f $name`;
`tar -xvf $pg.tar`;
chdir $pg;
`chmod u+x *`;
......@@ -1212,9 +1285,11 @@ sub install_binary_package
}
chdir $base;
$PG{$pg}{from_binary}=1;
return &pg_is_installed ($pg, $BIN);
}
################################################################################
# #
# #
......@@ -1478,6 +1553,29 @@ sub supported_os
return $SUPPORTED_OS{$os};
}
sub add2env_file
{
my ($env, $var, $value)=(@_);
my $F = new FileHandle;
my $t;
if (!$value){return;}
#make sure new variables do not get duplicated
if ( -e $env)
{
open ($F, "$env");
while (<$F>)
{
my $line=$_;
if (!($line=~/$var/)){$t.=$line;}
}
close ($F);
}
$t.="$var=$value\n";
open ($F, ">$env");
print $F "$t";
$ENV{$var}=$value;
close ($F);
}
################################################################################
# #
......@@ -1545,8 +1643,9 @@ $PG{"t_coffee"}{"type"}="sequence_multiple_aligner";
$PG{"t_coffee"}{"ADDRESS"}="http://www.tcoffee.org";
$PG{"t_coffee"}{"language"}="C++";
$PG{"t_coffee"}{"language2"}="CXX";
$PG{"t_coffee"}{"source"}="http://www.tcoffee.org/Packages/Stable/Latest/T-COFFEE_distribution.tar.gz";
$PG{"t_coffee"}{"source"}="http://www.tcoffee.org/Packages/sources/tcoffee/stable/T-COFFEE_distribution.tar.gz";
$PG{"t_coffee"}{"update_action"}="always";
$PG{"t_coffee"}{"binary"}="t_coffee";
$PG{"t_coffee"}{"mode"}="tcoffee,mcoffee,rcoffee,expresso,3dcoffee";
$PG{"clustalo"}{"4_TCOFFEE"}="CLUSTALO";
$PG{"clustalo"}{"type"}="sequence_multiple_aligner";
......@@ -1565,6 +1664,7 @@ $PG{"strike"}{"language2"}="CXX";
$PG{"strike"}{"source"}="http://www.tcoffee.org/Projects/strike/strike_v1.2.tar.bz2";
$PG{"strike"}{"mode"}="tcoffee,expresso";
$PG{"strike"}{"version"}="1.2";
$PG{"strike"}{"binary"}="strike";
$PG{"clustalw2"}{"4_TCOFFEE"}="CLUSTALW2";
$PG{"clustalw2"}{"type"}="sequence_multiple_aligner";
$PG{"clustalw2"}{"ADDRESS"}="http://www.clustal.org";
......@@ -1572,6 +1672,7 @@ $PG{"clustalw2"}{"language"}="C++";
$PG{"clustalw2"}{"language2"}="CXX";
$PG{"clustalw2"}{"source"}="http://www.clustal.org/download/2.0.10/clustalw-2.0.10-src.tar.gz";
$PG{"clustalw2"}{"mode"}="mcoffee,rcoffee";
$PG{"clustalw2"}{"binary"}="clustalw2";
$PG{"clustalw2"}{"version"}="2.0.10";
$PG{"clustalw"}{"4_TCOFFEE"}="CLUSTALW";
$PG{"clustalw"}{"type"}="sequence_multiple_aligner";
......@@ -1581,6 +1682,7 @@ $PG{"clustalw"}{"language2"}="C";
$PG{"clustalw"}{"source"}="http://www.clustal.org/download/1.X/ftp-igbmc.u-strasbg.fr/pub/ClustalW/clustalw1.82.UNIX.tar.gz";
$PG{"clustalw"}{"mode"}="mcoffee,rcoffee";
$PG{"clustalw"}{"version"}="1.82";
$PG{"clustalw"}{"binary"}="clustalw";
$PG{"dialign-t"}{"4_TCOFFEE"}="DIALIGNT";
$PG{"dialign-t"}{"type"}="sequence_multiple_aligner";
$PG{"dialign-t"}{"ADDRESS"}="http://dialign-tx.gobics.de/";
......@@ -1729,6 +1831,7 @@ $PG{"sap"}{"language2"}="C";
$PG{"sap"}{"source"}="https://github.com/jkleinj/SAP/archive/v.1.1.3.tar.gz";
$PG{"sap"}{"mode"}="expresso,3dcoffee";
$PG{"sap"}{"version"}="1.1.3";
$PG{"sap"}{"binary"}="sap";
$PG{"TMalign"}{"4_TCOFFEE"}="TMALIGN";
$PG{"TMalign"}{"type"}="structure_pairwise_aligner";
$PG{"TMalign"}{"ADDRESS"}="http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign.f";
......@@ -1821,7 +1924,7 @@ $PG{"hmmtop"}{"language2"}="C";
$PG{"hmmtop"}{"source"}="http://www.tcoffee.org/Packages/mirrors/hmmtop2.1.tgz";
$PG{"hmmtop"}{"binary"}="hmmtop";
$PG{"hmmtop"}{"update_action"}="never";
$PG{"hmmtop"}{"mode"}="tcoffee";
$PG{"hmmtop"}{"mode"}="psicoffee";
$PG{"hmmtop"}{"version"}="2.1";
$PG{"gorIV"}{"4_TCOFFEE"}="GOR4";
$PG{"gorIV"}{"type"}="protein_secondarystructure_predictor";
......@@ -1880,7 +1983,7 @@ $PG{"XML::Simple"}{"language"}="Perl";
$PG{"XML::Simple"}{"language2"}="Perl";
$PG{"XML::Simple"}{"source"}="empty";
$PG{"XML::Simple"}{"mode"}="psicoffee,expresso,accurate";
$PG{"x3dna"}{"4_TCOFFEE"}="x3dna-ssr";
$PG{"x3dna"}{"4_TCOFFEE"}="x3dna";
$PG{"x3dna"}{"type"}="RNA_secondarystructure_predictor";
$PG{"x3dna"}{"ADDRESS"}="http://x3dna.bio.columbia.edu/";
$PG{"x3dna"}{"source"}="http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz";
......@@ -1949,7 +2052,7 @@ $PG{Fortran}{type}="compiler";
$PG{Perl}{compiler}="CPAN";
$PG{Perl}{type}="compiler";
$SUPPORTED_OS{macox}="Macintosh";
$SUPPORTED_OS{macosx}="Macintosh";
$SUPPORTED_OS{linux}="Linux";
$SUPPORTED_OS{windows}="Cygwin";
......
license.txt
View file @ ba720c2d
-------------------------------COPYRIGHT NOTICE------------------------------/
ACADEMIC LICENCE AGREEMENT
© Centro de Regulacio Genomica and Cedric Notredame ( 11 Dec 2018 - 09:27).
© Centro de Regulacio Genomica and Cedric Notredame ( 30 Jul 2019 - 01:49).
GNU GENERAL PUBLIC LICENSE
Version 2, June 1991
......
t_coffee_source/coffee_defines.h
View file @ ba720c2d
......@@ -2,7 +2,7 @@
/* (c) Centro de Regulacio Genomica */
/* and */
/* Cedric Notredame */
/* 11 Dec 2018 - 09:27. */
/* 30 Jul 2019 - 01:49. */
/*All rights reserved. */
/*This file is part of T-COFFEE. */
/* */
......
t_coffee_source/data_headers/perl_header_lib.h
View file @ ba720c2d
......@@ -2,7 +2,7 @@
/* (c) Centro de Regulacio Genomica */
/* and */
/* Cedric Notredame */
/* 11 Dec 2018 - 09:27. */
/* 30 Jul 2019 - 01:49. */
/*All rights reserved. */
/*This file is part of T-COFFEE. */
/* */
......
t_coffee_source/data_headers/programmes_define.h
View file @ ba720c2d
......@@ -2,7 +2,7 @@
/* (c) Centro de Regulacio Genomica */
/* and */
/* Cedric Notredame */
/* 11 Dec 2018 - 09:27. */
/* 30 Jul 2019 - 01:49. */
/*All rights reserved. */
/*This file is part of T-COFFEE. */
/* */
......
t_coffee_source/define_header.h
View file @ ba720c2d
......@@ -2,7 +2,7 @@
/* (c) Centro de Regulacio Genomica */
/* and */
/* Cedric Notredame */
/* 11 Dec 2018 - 09:27. */
/* 30 Jul 2019 - 01:49. */
/*All rights reserved. */
/*This file is part of T-COFFEE. */
/* */
......@@ -34,9 +34,9 @@
// the following constants are updated during the build process -- see the 'makefile' for details
#define PROGRAM "T-COFFEE"
#define AUTHOR "Cedric Notredame "
#define DATE "11 Dec 2018 - 09:27"
#define VERSION "Version_12.00.7fb08c2"
#define BUILD_INFO "2018-12-11 09:27:12 - Revision 7fb08c2 - Build 211"
#define DATE "30 Jul 2019 - 01:49"
#define VERSION "Version_13.30.0.6a5203f"
#define BUILD_INFO "2019-07-30 01:49:30 - Revision 9900b56 - Build 399"
#define DISTRIBUTION_ADDRESS "www.tcoffee.org/Packages"
......
t_coffee_source/dev1_lib_header.h
View file @ ba720c2d
......@@ -2,7 +2,7 @@
/* (c) Centro de Regulacio Genomica */
/* and */
/* Cedric Notredame */
/* 11 Dec 2018 - 09:27. */
/* 30 Jul 2019 - 01:49. */
/*All rights reserved. */
/*This file is part of T-COFFEE. */
/* */
......
t_coffee_source/dev_lib/dev1.c
View file @ ba720c2d
......@@ -2,7 +2,7 @@
/* (c) Centro de Regulacio Genomica */
/* and */
/* Cedric Notredame */
/* 11 Dec 2018 - 09:27. */
/* 30 Jul 2019 - 01:49. */
/*All rights reserved. */
/*This file is part of T-COFFEE. */
/* */
......
t_coffee_source/dev_lib/dev1.h
View file @ ba720c2d
......@@ -2,7 +2,7 @@
/* (c) Centro de Regulacio Genomica */
/* and */
/* Cedric Notredame */
/* 11 Dec 2018 - 09:27. */
/* 30 Jul 2019 - 01:49. */
/*All rights reserved. */
/*This file is part of T-COFFEE. */
/* */
......
t_coffee_source/dp_lib/CUSTOM_evaluate_for_struc.c
View file @ ba720c2d
......@@ -2,7 +2,7 @@
/* (c) Centro de Regulacio Genomica */
/* and */
/* Cedric Notredame */
/* 11 Dec 2018 - 09:27. */
/* 30 Jul 2019 - 01:49. */
/*All rights reserved. */
/*This file is part of T-COFFEE. */
/* */
......
t_coffee_source/dp_lib/CUSTOM_evaluate_for_struc.h
View file @ ba720c2d
......@@ -2,7 +2,7 @@
/* (c) Centro de Regulacio Genomica */
/* and */
/* Cedric Notredame */
/* 11 Dec 2018 - 09:27. */
/* 30 Jul 2019 - 01:49. */
/*All rights reserved. */
/*This file is part of T-COFFEE. */
/* */
......