Info2: <<
Package: tcoffee
Version: 13.45.0.4846264
# WARNING: the install *really* wants to download files from various
# websites, and each new version seems to need different tricks or
# pathnames to prevent that from happening.
Revision: 102
Distribution: 10.9
Type: systemperl (5.16.2), gcc (11)
Source: http://www.tcoffee.org/Packages/Stable/Latest/T-COFFEE_distribution_Version_%v.tar.gz
Source-Checksum: SHA256(c8e5ba17de11ddf07cf2ed37f077d81c1432d55b77761f115f9374de6f8d0d03)
Source2: http://www.tcoffee.org/Projects/strike/strike_v1.2.tar.bz2
Source2-Checksum: SHA256(4e0974c57a18b10faff635f60d2d4c5e253a67e43e525aec98545f45884e7295)
Depends: <<
	gcc%type_pkg[gcc]-shlibs,
	system-perl%type_pkg[systemperl],
	libwww-pm%type_pkg[systemperl],
	soap-lite-ssl-pm%type_pkg[systemperl] | soap-lite-pm%type_pkg[systemperl],
	xml-simple-pm%type_pkg[systemperl]
<<
BuildDepends: gcc%type_pkg[gcc]-compiler
PatchFile: %n.patch
PatchFile-MD5: 11faa02387ca99b69d7bb81d98a2b337
PatchScript: <<
	%{default_script}

	perl -pi -e 's|f77|%p/bin/gfortran-fsf-%type_pkg[gcc]|g' install
	perl -pi -e 's|=\"gcc\"|=\"%p/bin/gcc-fsf-%type_pkg[gcc]\"|g' install
	perl -pi -e 's|=\"g\+\+\"|=\"%p/bin/g++-fsf-%type_pkg[gcc]\"|g' install
	perl -pi -e 's|CC=g\+\+|CC=%p/bin/g++-fsf-%type_pkg[gcc]|g' t_coffee_source/makefile
	perl -pi -e 's|CC =g\+\+|CC =%p/bin/g++-fsf-%type_pkg[gcc]|g' ../strike_v1.2/Makefile

	perl -pi -e 's|/usr/local/bin|%p/bin|g ' install

	# Make sure we get a deterministic perl interp, so we can set
	# matching perl-versioned -pmXXX dependencies.
	perl -pi -e 's|"perl |"/usr/bin/perl |g' t_coffee_source/*.[ch]
	perl -pi -e 's,/usr/bin/env perl,/usr/bin/perl,' example/*

	# Source2ExtractDir would leave these files as owned by root (fink bug?)
	mkdir -p bin/cache/download/distributions/strike
	cp -pr ../strike_v1.2  bin/cache/download/distributions/strike
<<
SetCC: %p/bin/gcc-fsf-%type_pkg[gcc]
CompileScript: <<
	./install tcoffee -exec=%p/bin -plugins=%p/bin -nobinaries -recompile
<<

InstallScript: <<
 mkdir -p %i/bin
 cp t_coffee_source/t_coffee %i/bin

 mkdir -p %i/share/%n
 cp -R example %i/share/%n
<<

DocFiles: license.txt
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.
<<
DescPackaging: <<
Previous maintainer: Jason Stajich
                     Koen van der Drift <driftkop@users.sourceforge.net>
<<
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: None <fink-devel@lists.sourceforge.net>
Homepage: http://www.tcoffee.org/Projects/tcoffee/index.html
<<