diff -u -r BioPerl-1.6.1/Bio/Variation/IO.pm BioPerl-1.6.1.mod/Bio/Variation/IO.pm
--- BioPerl-1.6.1/Bio/Variation/IO.pm 2007-02-14 04:37:48.000000000 -0700
+++ BioPerl-1.6.1.mod/Bio/Variation/IO.pm 2008-09-25 02:03:26.000000000 -0700
@@ -86,7 +86,7 @@
This makes the simplest ever reformatter
- #!/usr/local/bin/perl
+ #!/usr/bin/perl
$format1 = shift;
$format2 = shift;
Only in BioPerl-1.6.1.mod/Bio/Variation: IO.pm.orig
diff -u -r BioPerl-1.6.1/Build.PL BioPerl-1.6.1.mod/Build.PL
--- BioPerl-1.6.1/Build.PL 2009-09-29 12:33:45.000000000 -0400
+++ BioPerl-1.6.1.mod/Build.PL 2009-11-11 22:23:17.000000000 -0500
@@ -31,13 +31,13 @@
'DB_File' => 0,
'Data::Stag' => 0.11, # Bio::SeqIO::swiss, we can change to 'recommend' if needed
'Scalar::Util' => 0, # not in Perl 5.6.1, arrived in core in 5.7.3
- 'ExtUtils::Manifest' => '1.52', # allows spaces in file names
+# 'ExtUtils::Manifest' => '1.52', # allows spaces in file names
},
build_requires => {
'Test::More' => 0,
'Module::Build' => 0.2805,
- 'Test::Harness' => 2.62,
- 'CPAN' => 1.81
+# 'Test::Harness' => 2.62,
+# 'CPAN' => 1.81
},
recommends => { # does what you would expect of recommends, except more informative output and generates optional_features in META.yml
'Ace' => '0/access of ACeDB database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace',
diff -u -r BioPerl-1.6.1/examples/align/align_on_codons.pl BioPerl-1.6.1.mod/examples/align/align_on_codons.pl
--- BioPerl-1.6.1/examples/align/align_on_codons.pl 2007-02-14 04:37:47.000000000 -0700
+++ BioPerl-1.6.1.mod/examples/align/align_on_codons.pl 2008-09-25 02:03:26.000000000 -0700
@@ -13,10 +13,10 @@
BEGIN {
$CODONSIZE = 3; # parametrize everything like a good little programmer
if( ! defined $ENV{'CLUSTALDIR'} ) {
- $ENV{'CLUSTALDIR'} = '/usr/local/bin';
+ $ENV{'CLUSTALDIR'} = '/usr/bin';
}
if( ! defined $ENV{'TCOFFEEDIR'} ) {
- $ENV{'TCOFFEEDIR'} = '/usr/local/bin';
+ $ENV{'TCOFFEEDIR'} = '/usr/bin';
}
$USAGE =
qq{align_on_codons.pl < file.fa
diff -u -r BioPerl-1.6.1/examples/db/dbfetch BioPerl-1.6.1.mod/examples/db/dbfetch
--- BioPerl-1.6.1/examples/db/dbfetch 2007-02-14 04:37:48.000000000 -0700
+++ BioPerl-1.6.1.mod/examples/db/dbfetch 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -- # -*-Perl-*-
+#!/usr/bin/perl -- # -*-Perl-*-
=head1 NAME
diff -u -r BioPerl-1.6.1/examples/db/getGenBank.pl BioPerl-1.6.1.mod/examples/db/getGenBank.pl
--- BioPerl-1.6.1/examples/db/getGenBank.pl 2007-02-14 04:37:47.000000000 -0700
+++ BioPerl-1.6.1.mod/examples/db/getGenBank.pl 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
#
# How to retrieve GenBank entries over the Web
#
diff -u -r BioPerl-1.6.1/examples/db/get_seqs.pl BioPerl-1.6.1.mod/examples/db/get_seqs.pl
--- BioPerl-1.6.1/examples/db/get_seqs.pl 2007-02-14 04:37:48.000000000 -0700
+++ BioPerl-1.6.1.mod/examples/db/get_seqs.pl 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
use strict;
use vars qw($USAGE);
use Carp;
diff -u -r BioPerl-1.6.1/examples/generate_random_seq.pl BioPerl-1.6.1.mod/examples/generate_random_seq.pl
--- BioPerl-1.6.1/examples/generate_random_seq.pl 2007-02-14 04:37:47.000000000 -0700
+++ BioPerl-1.6.1.mod/examples/generate_random_seq.pl 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/bin/perl -w
+#!/usr/bin/perl -w
use strict;
use vars qw($USAGE);
diff -u -r BioPerl-1.6.1/examples/searchio/psiblast_features.pl BioPerl-1.6.1.mod/examples/searchio/psiblast_features.pl
--- BioPerl-1.6.1/examples/searchio/psiblast_features.pl 2007-02-14 04:37:48.000000000 -0700
+++ BioPerl-1.6.1.mod/examples/searchio/psiblast_features.pl 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
# Example usage of a SearchIO::psiblast parser of traditional format Blast
# and PSI-Blast reports.
diff -u -r BioPerl-1.6.1/examples/structure/structure-io.pl BioPerl-1.6.1.mod/examples/structure/structure-io.pl
--- BioPerl-1.6.1/examples/structure/structure-io.pl 2007-02-14 04:37:48.000000000 -0700
+++ BioPerl-1.6.1.mod/examples/structure/structure-io.pl 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/bin/perl -w
+#!/usr/bin/perl -w
# Getting Entry, Chain, Residue, and Atom objects given a PDB file
use Bio::Structure::IO;
diff -u -r BioPerl-1.6.1/examples/tk/hitdisplay.pl BioPerl-1.6.1.mod/examples/tk/hitdisplay.pl
--- BioPerl-1.6.1/examples/tk/hitdisplay.pl 2007-02-14 04:37:47.000000000 -0700
+++ BioPerl-1.6.1.mod/examples/tk/hitdisplay.pl 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
#
# PROGRAM : hitdisplay.pl
# PURPOSE : Demonstrate Bio::Tk::HitDisplay
diff -u -r BioPerl-1.6.1/examples/tools/gb_to_gff.pl BioPerl-1.6.1.mod/examples/tools/gb_to_gff.pl
--- BioPerl-1.6.1/examples/tools/gb_to_gff.pl 2007-02-14 04:37:47.000000000 -0700
+++ BioPerl-1.6.1.mod/examples/tools/gb_to_gff.pl 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
use strict;
use Bio::Tools::GFF;
diff -u -r BioPerl-1.6.1/examples/tools/gff2ps.pl BioPerl-1.6.1.mod/examples/tools/gff2ps.pl
--- BioPerl-1.6.1/examples/tools/gff2ps.pl 2007-02-14 04:37:47.000000000 -0700
+++ BioPerl-1.6.1.mod/examples/tools/gff2ps.pl 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
=head1 NAME
--- BioPerl-1.6.1/MANIFEST.orig 2008-12-27 20:29:43.000000000 -0700
+++ BioPerl-1.6.1/MANIFEST 2008-12-27 20:31:23.000000000 -0700
@@ -424,15 +424,6 @@
Bio/Phenotype/OMIM/OMIMparser.pm
Bio/Phenotype/Phenotype.pm
Bio/Phenotype/PhenotypeI.pm
-Bio/PhyloNetwork.pm
-Bio/PhyloNetwork/Factory.pm
-Bio/PhyloNetwork/FactoryX.pm
-Bio/PhyloNetwork/GraphViz.pm
-Bio/PhyloNetwork/muVector.pm
-Bio/PhyloNetwork/RandomFactory.pm
-Bio/PhyloNetwork/TreeFactory.pm
-Bio/PhyloNetwork/TreeFactoryMulti.pm
-Bio/PhyloNetwork/TreeFactoryX.pm
Bio/PopGen/Genotype.pm
Bio/PopGen/GenotypeI.pm
Bio/PopGen/HtSNP.pm
@@ -1994,12 +1985,6 @@
t/Tools/tRNAscanSE.t
t/Tree/Compatible.t
t/Tree/Node.t
-t/Tree/PhyloNetwork/Factory.t
-t/Tree/PhyloNetwork/GraphViz.t
-t/Tree/PhyloNetwork/MuVector.t
-t/Tree/PhyloNetwork/PhyloNetwork.t
-t/Tree/PhyloNetwork/RandomFactory.t
-t/Tree/PhyloNetwork/TreeFactory.t
t/Tree/RandomTreeFactory.t
t/Tree/Tree.t
t/Tree/TreeIO.t
