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; + ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Fink-commits mailing list Fink-commits@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.cvs