Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv16152
Modified Files:
tcoffee.patch
Added Files:
tcoffee-10.4.info tcoffee-10.5.info
Log Message:
new upstream
--- NEW FILE: tcoffee-10.4.info ---
Package: tcoffee
Version: 6.92
Revision: 1
Distribution: 10.4
Source: http://www.tcoffee.org/Packages/T-COFFEE_distribution_Version_%v.tar.gz
Source-MD5: 4b53786aa577518b08fe068e2863ce9e
#Source2: http://probcons.stanford.edu/probconsRNA.tar.gz
#Source2-MD5: 2aa13012124208ca5dd6b0a1d508208d
#Source2ExtractDir: T-COFFEE_distribution_Version_%v/Downloads/files/
#Source3:
http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.603-with-extensions-src.tgz
#Source3-MD5: 3085861cdd2eb4bd8f9b4e0849744297
#Source3ExtractDir: T-COFFEE_distribution_Version_%v/Downloads/files/
Sourcedirectory: T-COFFEE_distribution_Version_%v
Depends: g77, soap-lite-pm586
Patch: %n.patch
CompileScript: <<
#!/bin/bash -ev
# mkdir -p T-COFFEE_distribution_Version_%v/Downloads/files
# cp %p/src/probconsRNA.tar.gz Downloads/files/
./install tcoffee -path=%p
<<
InstallScript: <<
mkdir -p %i/bin
cp bin/macosx/* %i/bin
mkdir -p %i/share/%n
cp -R example html %i/share/%n
<<
DocFiles: doc/* license.txt
#RuntimeVars: <<
# CLUSTALW_4_TCOFFEE: %p/bin/clustalw
#<<
Description: T-Coffee Multiple Sequence Alignment Program
DescDetail: <<
T-Coffee computes multiple sequence alignments for protein or dna/rna
sequences. It is considerably slower than ClustalW but does a better
job aligning more distantly related sequences (<30% identity). There
are also some enhancements for cDNA alignments.
Previous maintainer: Jason Stajich
<<
DescUsage: <<
Before running T-coffee, issue the following two commands:
cp -R %p/share/%n/t_coffee/ ~/.t_coffee
sudo chown -R <your_username> ~/.t_coffee/
T-coffee can be started by the command t_coffee.
<<
License: GPL
Maintainer: Koen van der Drift <[EMAIL PROTECTED]>
Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
--- NEW FILE: tcoffee-10.5.info ---
Package: tcoffee
Version: 6.92
Revision: 1
Distribution: 10.5
Source: http://www.tcoffee.org/Packages/T-COFFEE_distribution_Version_%v.tar.gz
Source-MD5: 4b53786aa577518b08fe068e2863ce9e
#Source2: http://probcons.stanford.edu/probconsRNA.tar.gz
#Source2-MD5: 2aa13012124208ca5dd6b0a1d508208d
#Source2ExtractDir: T-COFFEE_distribution_Version_%v/Downloads/files/
#Source3:
http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.603-with-extensions-src.tgz
#Source3-MD5: 3085861cdd2eb4bd8f9b4e0849744297
#Source3ExtractDir: T-COFFEE_distribution_Version_%v/Downloads/files/
Sourcedirectory: T-COFFEE_distribution_Version_%v
Depends: g77, soap-lite-pm588
Patch: %n.patch
CompileScript: <<
#!/bin/bash -ev
# mkdir -p T-COFFEE_distribution_Version_%v/Downloads/files
# cp %p/src/probconsRNA.tar.gz Downloads/files/
./install tcoffee -path=%p
<<
InstallScript: <<
mkdir -p %i/bin
cp bin/macosx/* %i/bin
mkdir -p %i/share/%n
cp -R example html %i/share/%n
<<
DocFiles: doc/* license.txt
#RuntimeVars: <<
# CLUSTALW_4_TCOFFEE: %p/bin/clustalw
#<<
Description: T-Coffee Multiple Sequence Alignment Program
DescDetail: <<
T-Coffee computes multiple sequence alignments for protein or dna/rna
sequences. It is considerably slower than ClustalW but does a better
job aligning more distantly related sequences (<30% identity). There
are also some enhancements for cDNA alignments.
Previous maintainer: Jason Stajich
<<
DescUsage: <<
Before running T-coffee, issue the following two commands:
cp -R %p/share/%n/t_coffee/ ~/.t_coffee
sudo chown -R <your_username> ~/.t_coffee/
T-coffee can be started by the command t_coffee.
<<
License: GPL
Maintainer: Koen van der Drift <[EMAIL PROTECTED]>
Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
Index: tcoffee.patch
===================================================================
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/tcoffee.patch,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -d -r1.6 -r1.7
--- tcoffee.patch 26 Oct 2007 02:10:26 -0000 1.6
+++ tcoffee.patch 29 Sep 2008 00:27:02 -0000 1.7
@@ -1,57 +1,36 @@
-diff -Naur
T-COFFEE_distribution_Version_5.29/t_coffee_source/CUSTOM_evaluate_for_struc.c
T-COFFEE_distribution_Version_5.29-patched/t_coffee_source/CUSTOM_evaluate_for_struc.c
----
T-COFFEE_distribution_Version_5.29/t_coffee_source/CUSTOM_evaluate_for_struc.c
2007-01-30 12:22:25.000000000 -0500
-+++
T-COFFEE_distribution_Version_5.29-patched/t_coffee_source/CUSTOM_evaluate_for_struc.c
2007-02-17 07:54:41.000000000 -0500
-@@ -3,6 +3,7 @@
- #include <math.h>
- #include <stdarg.h>
-
-+#include <string.h>
-
- #include "io_lib_header.h"
- #include "util_lib_header.h"
-diff -Naur
T-COFFEE_distribution_Version_5.29/t_coffee_source/evaluate_for_struc.c
T-COFFEE_distribution_Version_5.29-patched/t_coffee_source/evaluate_for_struc.c
---- T-COFFEE_distribution_Version_5.29/t_coffee_source/evaluate_for_struc.c
2007-01-30 12:22:26.000000000 -0500
-+++
T-COFFEE_distribution_Version_5.29-patched/t_coffee_source/evaluate_for_struc.c
2007-02-17 07:55:59.000000000 -0500
-@@ -4,6 +4,8 @@
- #include <stdarg.h>
- #include <ctype.h>
-
-+#include <string.h>
-+
- #include "io_lib_header.h"
- #include "util_lib_header.h"
- #include "define_header.h"
-diff -Naur T-COFFEE_distribution_Version_5.29/t_coffee_source/hsearch.c
T-COFFEE_distribution_Version_5.29-patched/t_coffee_source/hsearch.c
---- T-COFFEE_distribution_Version_5.29/t_coffee_source/hsearch.c
2007-01-30 12:22:26.000000000 -0500
-+++ T-COFFEE_distribution_Version_5.29-patched/t_coffee_source/hsearch.c
2007-02-17 07:56:16.000000000 -0500
-@@ -4,6 +4,7 @@
- #include <math.h>
- #include <stdarg.h>
-
-+#include <string.h>
-
- #include "io_lib_header.h"
- #include "util_lib_header.h"
-diff -Naur
T-COFFEE_distribution_Version_5.29/t_coffee_source/util_dp_fasta_sw.c
T-COFFEE_distribution_Version_5.29-patched/t_coffee_source/util_dp_fasta_sw.c
---- T-COFFEE_distribution_Version_5.29/t_coffee_source/util_dp_fasta_sw.c
2007-01-30 12:22:30.000000000 -0500
-+++
T-COFFEE_distribution_Version_5.29-patched/t_coffee_source/util_dp_fasta_sw.c
2007-02-17 08:02:38.000000000 -0500
-@@ -3,6 +3,7 @@
- #include <math.h>
- #include <stdarg.h>
-
-+#include <string.h>
+diff -Naur T-COFFEE_distribution_Version_6.92/install
T-COFFEE_distribution_Version_6.92-patched/install
+--- T-COFFEE_distribution_Version_6.92/install 2008-09-12 05:58:43.000000000
-0400
++++ T-COFFEE_distribution_Version_6.92-patched/install 2008-09-27
16:15:15.000000000 -0400
+@@ -233,11 +233,11 @@
+ }
+ }
+ print "------- Finishing The installation\n";
+-if ( &input_yes("??????? Do you want to finalize the installation and copy
the executables to their final destination ? ([y]/n):"))
+- {
+-
$installation_directory=&input_installation_directory($installation_directory);
+- $final_report=&install ($installation_directory);
+- }
++#if ( &input_yes("??????? Do you want to finalize the installation and copy
the executables to their final destination ? ([y]/n):"))
++# {
++#
$installation_directory=&input_installation_directory($installation_directory);
++# $final_report=&install ($installation_directory);
++# }
- #include "io_lib_header.h"
- #include "util_lib_header.h"
-diff -Naur T-COFFEE_distribution_Version_5.29/t_coffee_source/util_make_tree.c
T-COFFEE_distribution_Version_5.29-patched/t_coffee_source/util_make_tree.c
---- T-COFFEE_distribution_Version_5.29/t_coffee_source/util_make_tree.c
2007-01-30 12:22:31.000000000 -0500
-+++
T-COFFEE_distribution_Version_5.29-patched/t_coffee_source/util_make_tree.c
2007-02-17 08:04:02.000000000 -0500
-@@ -3,6 +3,8 @@
- #include <math.h>
- #include <stdarg.h>
+ print "\n";
+ print
"*********************************************************************\n";
+@@ -458,6 +458,7 @@
-+#include <string.h>
-+
- #include "io_lib_header.h"
- #include "util_lib_header.h"
- #include "dp_lib_header.h"
+ sub sign_license
+ {
++ return 0;
+ my ($signature_file,$signature_flag, $email)=(@_);
+
+ if (!-e $signature_file || !-e $signature_flag)
+@@ -500,6 +501,7 @@
+
+ sub get_email
+ {
++ return 0;
+ my ($tcdir, $email)=(@_);
+ my $answer;
+
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