rpms/perl-bioperl/devel bioperl-1.5.0-paths.patch, NONE, 1.1 filter-requires.sh, NONE, 1.1 perl-bioperl.spec, NONE, 1.1 .cvsignore, 1.1, 1.2 sources, 1.1, 1.2
Tom Callaway (spot)
fedora-extras-commits at redhat.com
Mon Apr 11 22:50:23 UTC 2005
Author: spot
Update of /cvs/extras/rpms/perl-bioperl/devel
In directory cvs-int.fedora.redhat.com:/tmp/cvs-serv29114/devel
Modified Files:
.cvsignore sources
Added Files:
bioperl-1.5.0-paths.patch filter-requires.sh perl-bioperl.spec
Log Message:
auto-import perl-bioperl-1.5.0-3 on branch devel from perl-bioperl-1.5.0-3.src.rpm
bioperl-1.5.0-paths.patch:
--- NEW FILE bioperl-1.5.0-paths.patch ---
diff -ru bioperl-1.5.0.orig/Bio/Variation/IO.pm bioperl-1.5.0/Bio/Variation/IO.pm
--- bioperl-1.5.0.orig/Bio/Variation/IO.pm 2003-06-04 04:36:44.000000000 -0400
+++ bioperl-1.5.0/Bio/Variation/IO.pm 2005-03-21 20:21:54.000000000 -0500
@@ -83,7 +83,7 @@
This makes the simplest ever reformatter
- #!/usr/local/bin/perl
+ #!/usr/bin/perl
$format1 = shift;
$format2 = shift || die "Usage: reformat format1 format2 < input > output";
diff -ru bioperl-1.5.0.orig/bioperl.lisp bioperl-1.5.0/bioperl.lisp
--- bioperl-1.5.0.orig/bioperl.lisp 2003-03-05 22:41:24.000000000 -0500
+++ bioperl-1.5.0/bioperl.lisp 2005-03-21 20:23:49.000000000 -0500
@@ -13,7 +13,7 @@
"Places #!..perl at the start of the script"
(interactive)
(goto-char (point-min))
- (insert "#!/usr/local/bin/perl\n"))
+ (insert "#!/usr/bin/perl\n"))
(defun bioperl-object-start (perl-object-name perl-caretaker-name caretaker-email)
diff -ru bioperl-1.5.0.orig/doc/howto/html/SeqIO.html bioperl-1.5.0/doc/howto/html/SeqIO.html
--- bioperl-1.5.0.orig/doc/howto/html/SeqIO.html 2004-10-28 17:16:51.000000000 -0400
+++ bioperl-1.5.0/doc/howto/html/SeqIO.html 2005-03-21 20:27:13.000000000 -0500
@@ -22,7 +22,7 @@
first lines of your script might look like:
</p><p>
<pre class="programlisting">
-#!/bin/perl
+#!/usr/bin/perl
use Bio::SeqIO;
my $file = shift; # get the file name, somehow
@@ -403,7 +403,7 @@
my $outfile = shift or die $usage;
# create one SeqIO object to read in, and another to write out
- my $seqin = Bio::SeqIO->new(-file => "/usr/local/bin/gunzip -c $infile |",
+ my $seqin = Bio::SeqIO->new(-file => "/usr/bin/gunzip -c $infile |",
-format => $informat);
my $seqout = Bio::SeqIO->new(-file => ">$outfile",
@@ -442,7 +442,7 @@
my $seqin = Bio::SeqIO->new(-file => "<$infile",
-format => $informat);
my $seqout = Bio::SeqIO->new(-file =>
- "| /usr/local/bin/xdformat -o $outdbname -${outdbtype} -- -",
+ "| /usr/bin/xdformat -o $outdbname -${outdbtype} -- -",
-format => 'Fasta');
# write each entry in the input to the output
@@ -547,7 +547,7 @@
were ready to run the program.
</p><p>
<pre class="programlisting">
- >perl -MBio::SeqIO -e 'my $gss = 0; my $in = Bio::SeqIO->new(q(-file) => q(/usr/local/bin/gunzip -c gbpri1.seq.gz |),
+ >perl -MBio::SeqIO -e 'my $gss = 0; my $in = Bio::SeqIO->new(q(-file) => q(/usr/bin/gunzip -c gbpri1.seq.gz |),
q(-format) => q(Genbank)); while (my $seq = $in->next_seq) { $gss++ if ($seq->keywords =~ m/GSS/);}
print "There are $gss GSS sequences in gbpri1.seq.gz\n";'
</pre>
@@ -634,4 +634,4 @@
error will be caught. And, of course, you are going to "use strict" right?
</p></div></div><div xmlns="" id="customfooter">
BioPerl DocBook
-</div></body></html>
\ No newline at end of file
+</div></body></html>
diff -ru bioperl-1.5.0.orig/doc/howto/sgml/Beginners.xml bioperl-1.5.0/doc/howto/sgml/Beginners.xml
--- bioperl-1.5.0.orig/doc/howto/sgml/Beginners.xml 2005-01-23 22:26:15.000000000 -0500
+++ bioperl-1.5.0/doc/howto/sgml/Beginners.xml 2005-03-21 20:28:55.000000000 -0500
@@ -341,7 +341,7 @@
</para>
<para>
<programlisting>
->/bin/perl
+>/usr/bin/perl
</programlisting>
</para>
<para>
@@ -362,7 +362,7 @@
</para>
<para>
<programlisting>
-#!/bin/perl -w
+#!/usr/bin/perl -w
</programlisting>
</para>
<para>
@@ -399,7 +399,7 @@
</para>
<para>
<programlisting>
-#!/bin/perl -w
+#!/usr/bin/perl -w
use Bio::Seq;
</programlisting>
@@ -423,7 +423,7 @@
</para>
<para>
<programlisting>
-#!/bin/perl -w
+#!/usr/bin/perl -w
use Bio::Seq;
@@ -472,7 +472,7 @@
</para>
<para>
<programlisting>
-#!/bin/perl -w
+#!/usr/bin/perl -w
use Bio::Seq;
@@ -494,7 +494,7 @@
</para>
<para>
<programlisting>
-#!/bin/perl -w
+#!/usr/bin/perl -w
use Bio::Seq;
@@ -558,7 +558,7 @@
</para>
<para>
<programlisting>
-#!/bin/perl -w
+#!/usr/bin/perl -w
use Bio::Seq;
use Bio::SeqIO;
@@ -641,7 +641,7 @@
</para>
<para>
<programlisting>
-#!/bin/perl -w
+#!/usr/bin/perl -w
use Bio::SeqIO;
@@ -658,7 +658,7 @@
</para>
<para>
<programlisting>
-#!/bin/perl -w
+#!/usr/bin/perl -w
use Bio::SeqIO;
diff -ru bioperl-1.5.0.orig/doc/howto/sgml/SeqIO.xml bioperl-1.5.0/doc/howto/sgml/SeqIO.xml
--- bioperl-1.5.0.orig/doc/howto/sgml/SeqIO.xml 2005-01-03 08:00:33.000000000 -0500
+++ bioperl-1.5.0/doc/howto/sgml/SeqIO.xml 2005-03-21 20:27:38.000000000 -0500
@@ -73,7 +73,7 @@
</para>
<para>
<programlisting>
-#!/bin/perl
+#!/usr/bin/perl
use strict;
use Bio::SeqIO;
@@ -766,7 +766,7 @@
my $outfile = shift or die $usage;
# create one SeqIO object to read in, and another to write out
- my $seqin = Bio::SeqIO->new(-file => "/usr/local/bin/gunzip -c $infile |",
+ my $seqin = Bio::SeqIO->new(-file => "/usr/bin/gunzip -c $infile |",
-format => $informat);
my $seqout = Bio::SeqIO->new(-file => ">$outfile",
@@ -810,7 +810,7 @@
my $seqin = Bio::SeqIO->new(-file => "<$infile",
-format => $informat);
my $seqout = Bio::SeqIO->new(-file =>
- "| /usr/local/bin/xdformat -o $outdbname -${outdbtype} -- -",
+ "| /usr/bin/xdformat -o $outdbname -${outdbtype} -- -",
-format => 'Fasta');
# write each entry in the input to the output
@@ -924,7 +924,7 @@
</para>
<para>
<programlisting>
- >perl -MBio::SeqIO -e 'my $gss = 0; my $in = Bio::SeqIO->new(q(-file) => q(/usr/local/bin/gunzip -c gbpri1.seq.gz |),
+ >perl -MBio::SeqIO -e 'my $gss = 0; my $in = Bio::SeqIO->new(q(-file) => q(/usr/bin/gunzip -c gbpri1.seq.gz |),
q(-format) => q(Genbank)); while (my $seq = $in->next_seq) { $gss++ if ($seq->keywords =~ m/GSS/);}
print "There are $gss GSS sequences in gbpri1.seq.gz\n";'
</programlisting>
diff -ru bioperl-1.5.0.orig/doc/howto/txt/SeqIO.txt bioperl-1.5.0/doc/howto/txt/SeqIO.txt
--- bioperl-1.5.0.orig/doc/howto/txt/SeqIO.txt 2004-10-28 17:15:48.000000000 -0400
+++ bioperl-1.5.0/doc/howto/txt/SeqIO.txt 2005-03-21 20:27:31.000000000 -0500
@@ -53,7 +53,7 @@
A piece of advice: always use the module Bio::SeqIO! Here's what the
first lines of your script might look like:
-#!/bin/perl
+#!/usr/bin/perl
use Bio::SeqIO;
my $file = shift; # get the file name, somehow
@@ -465,7 +465,7 @@
my $outfile = shift or die $usage;
# create one SeqIO object to read in, and another to write out
- my $seqin = Bio::SeqIO->new(-file => "/usr/local/bin/gunzip -c $infile
+ my $seqin = Bio::SeqIO->new(-file => "/usr/bin/gunzip -c $infile
|",
-format => $informat);
@@ -504,7 +504,7 @@
my $seqin = Bio::SeqIO->new(-file => "<$infile",
-format => $informat);
my $seqout = Bio::SeqIO->new(-file =>
- "| /usr/local/bin/xdformat -o $outdbname -${outdbtype} -- -",
+ "| /usr/bin/xdformat -o $outdbname -${outdbtype} -- -",
-format => 'Fasta');
# write each entry in the input to the output
@@ -621,7 +621,7 @@
were ready to run the program.
>perl -MBio::SeqIO -e 'my $gss = 0; my $in = Bio::SeqIO->new(q(-file) =>
- q(/usr/local/bin/gunzip -c gbpri1.seq.gz |),
+ q(/usr/bin/gunzip -c gbpri1.seq.gz |),
q(-format) => q(Genbank)); while (my $seq = $in->next_seq) { $gss++ if ($
seq->keywords =~ m/GSS/);}
print "There are $gss GSS sequences in gbpri1.seq.gz\n";'
diff -ru bioperl-1.5.0.orig/examples/align/align_on_codons.pl bioperl-1.5.0/examples/align/align_on_codons.pl
--- bioperl-1.5.0.orig/examples/align/align_on_codons.pl 2003-07-07 14:20:58.000000000 -0400
+++ bioperl-1.5.0/examples/align/align_on_codons.pl 2005-03-21 20:24:44.000000000 -0500
@@ -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';
}
$USAGE =
qq{align_on_codons.pl < file.fa
diff -ru bioperl-1.5.0.orig/examples/db/dbfetch bioperl-1.5.0/examples/db/dbfetch
--- bioperl-1.5.0.orig/examples/db/dbfetch 2003-07-15 12:12:16.000000000 -0400
+++ bioperl-1.5.0/examples/db/dbfetch 2005-03-21 20:25:01.000000000 -0500
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -- # -*-Perl-*-
+#!/usr/bin/perl -- # -*-Perl-*-
=head1 NAME
diff -ru bioperl-1.5.0.orig/examples/db/getGenBank.pl bioperl-1.5.0/examples/db/getGenBank.pl
--- bioperl-1.5.0.orig/examples/db/getGenBank.pl 2003-07-07 14:20:59.000000000 -0400
+++ bioperl-1.5.0/examples/db/getGenBank.pl 2005-03-21 20:24:57.000000000 -0500
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
#
# How to retrieve GenBank entries over the Web
#
diff -ru bioperl-1.5.0.orig/examples/db/get_seqs.pl bioperl-1.5.0/examples/db/get_seqs.pl
--- bioperl-1.5.0.orig/examples/db/get_seqs.pl 2003-07-07 14:20:59.000000000 -0400
+++ bioperl-1.5.0/examples/db/get_seqs.pl 2005-03-21 20:24:53.000000000 -0500
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
use strict;
use vars qw($USAGE);
use Carp;
diff -ru bioperl-1.5.0.orig/examples/generate_random_seq.pl bioperl-1.5.0/examples/generate_random_seq.pl
--- bioperl-1.5.0.orig/examples/generate_random_seq.pl 2004-11-01 16:09:08.000000000 -0500
+++ bioperl-1.5.0/examples/generate_random_seq.pl 2005-03-21 20:27:23.000000000 -0500
@@ -1,4 +1,4 @@
-#!/bin/perl -w
+#!/usr/bin/perl -w
use strict;
use vars qw($USAGE);
diff -ru bioperl-1.5.0.orig/examples/searchio/psiblast_features.pl bioperl-1.5.0/examples/searchio/psiblast_features.pl
--- bioperl-1.5.0.orig/examples/searchio/psiblast_features.pl 2004-02-21 05:50:34.000000000 -0500
+++ bioperl-1.5.0/examples/searchio/psiblast_features.pl 2005-03-21 20:24:30.000000000 -0500
@@ -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 -ru bioperl-1.5.0.orig/examples/structure/structure-io.pl bioperl-1.5.0/examples/structure/structure-io.pl
--- bioperl-1.5.0.orig/examples/structure/structure-io.pl 2004-11-01 16:09:33.000000000 -0500
+++ bioperl-1.5.0/examples/structure/structure-io.pl 2005-03-21 20:27:17.000000000 -0500
@@ -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 -ru bioperl-1.5.0.orig/examples/tk/hitdisplay.pl bioperl-1.5.0/examples/tk/hitdisplay.pl
--- bioperl-1.5.0.orig/examples/tk/hitdisplay.pl 2003-07-07 14:20:59.000000000 -0400
+++ bioperl-1.5.0/examples/tk/hitdisplay.pl 2005-03-21 20:24:26.000000000 -0500
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
#
# PROGRAM : hitdisplay.pl
# PURPOSE : Demonstrate Bio::Tk::HitDisplay
diff -ru bioperl-1.5.0.orig/examples/tools/gb_to_gff.pl bioperl-1.5.0/examples/tools/gb_to_gff.pl
--- bioperl-1.5.0.orig/examples/tools/gb_to_gff.pl 2003-07-07 14:20:59.000000000 -0400
+++ bioperl-1.5.0/examples/tools/gb_to_gff.pl 2005-03-21 20:24:21.000000000 -0500
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
use strict;
use Bio::Tools::GFF;
diff -ru bioperl-1.5.0.orig/examples/tools/gff2ps.pl bioperl-1.5.0/examples/tools/gff2ps.pl
--- bioperl-1.5.0.orig/examples/tools/gff2ps.pl 2003-07-07 14:20:59.000000000 -0400
+++ bioperl-1.5.0/examples/tools/gff2ps.pl 2005-03-21 20:24:17.000000000 -0500
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
=head1 NAME
diff -ru bioperl-1.5.0.orig/scripts/utilities/remote_blast.PLS bioperl-1.5.0/scripts/utilities/remote_blast.PLS
--- bioperl-1.5.0.orig/scripts/utilities/remote_blast.PLS 2003-02-25 03:41:06.000000000 -0500
+++ bioperl-1.5.0/scripts/utilities/remote_blast.PLS 2005-03-21 20:24:12.000000000 -0500
@@ -8,7 +8,7 @@
# POD documentation - main docs after the code
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
use strict;
use vars qw($USAGE);
diff -ru bioperl-1.5.0.orig/t/Promoterwise.t bioperl-1.5.0/t/Promoterwise.t
--- bioperl-1.5.0.orig/t/Promoterwise.t 2003-03-10 13:21:03.000000000 -0500
+++ bioperl-1.5.0/t/Promoterwise.t 2005-03-21 20:24:04.000000000 -0500
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
# -*-Perl-*-
## Bioperl Test Harness Script for Modules
diff -ru bioperl-1.5.0.orig/t/testformats.pl bioperl-1.5.0/t/testformats.pl
--- bioperl-1.5.0.orig/t/testformats.pl 2001-06-29 17:17:02.000000000 -0400
+++ bioperl-1.5.0/t/testformats.pl 2005-03-21 20:24:00.000000000 -0500
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
use strict;
use Bio::SeqIO;
--- NEW FILE filter-requires.sh ---
#!/bin/sh
# Disable this script, rebuild rpm, attempt install, cut-n-paste unsatisfied
# dependancies here... Crude, but effective.
/usr/lib/rpm/perl.req $* | grep -v -f - << EOL
Ace
Bio::Factory::EMBOSS
Bio::Tools::Run::Alignment::Clustalw
Bio::Tools::Run::Alignment::TCoffee
Bio::Tools::Run::Phylo::Molphy::ProtML
Bio::Tools::Run::Phylo::Phylip::Neighbor
Bio::Tools::Run::Phylo::Phylip::ProtDist
Bio::Tools::Run::Phylo::Phylip::ProtPars
Cache::FileCache
Class::AutoClass
Clone
Data::Stag
Data::Stag::XMLWriter
GD::Text::Align
SVG::Graph
SVG::Graph::Data
SVG::Graph::Data::Node
SVG::Graph::Data::Tree
Tk
Tree::DAG_Node
XML::DOM::XPath
XML::SAX
XML::SAX::Base
XML::SAX::Writer
enum
srsperl
EOL
--- NEW FILE perl-bioperl.spec ---
Name: perl-bioperl
Version: 1.5.0
Release: 3
Summary: A package of public domain Perl tools for computational molecular biology.
Group: Development/Libraries
License: GPL or Artistic
URL: http://bioperl.org
Source0: http://bioperl.org/DIST/bioperl-1.5.0.tar.bz2
Source1: filter-requires.sh
Patch0: bioperl-1.5.0-paths.patch
BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
BuildArch: noarch
BuildRequires: perl >= 1:5.6.1
BuildRequires: perl-SVG perl-GD-SVG perl-DBD-MySQL perl-DBD-Pg perl-IO-stringy
Requires: perl(:MODULE_COMPAT_%(eval "`%{__perl} -V:version`"; echo $version))
%define __perl_requires %{SOURCE1}
%description
Bioperl is a package of public domain Perl tools for computational
molecular biology.
%prep
%setup -q -n bioperl-%{version}
%patch0 -p1
%build
%{__perl} Makefile.PL INSTALLDIRS=vendor << EOF
a
EOF
make %{?_smp_mflags}
%install
rm -rf $RPM_BUILD_ROOT
make pure_install PERL_INSTALL_ROOT=$RPM_BUILD_ROOT
find $RPM_BUILD_ROOT -type f -a \( -name .packlist \
-o \( -name '*.bs' -a -empty \) \) -exec rm -f {} ';'
find $RPM_BUILD_ROOT -type d -depth -exec rmdir {} 2>/dev/null ';'
%check || :
# This can take a long time - it hits sourceforge.net during the tests
# and at least a few of the tests are known to fail.
#make test || exit 0
exit 0
%clean
rm -rf $RPM_BUILD_ROOT
%files
%defattr(-,root,root,-)
%doc doc examples models scripts
%doc AUTHORS BUGS Changes DEPRECATED FAQ INSTALL LICENSE PLATFORMS README bptutorial.pl
%{_bindir}/*
%{perl_vendorlib}/*
#%{_mandir}/man3/*.3* # need to patch makefile to get these
%changelog
* Wed Apr 06 2005 Hunter Matthews <thm at duke.edu> 1.5.0-3
- Review suggestions from José Pedro Oliveira
* Mon Apr 01 2005 Hunter Matthews <thm at duke.edu> 1.5.0-2
- Added buildrequires and improved %doc entries from FE mailing list.
* Mon Mar 21 2005 Hunter Matthews <thm at duke.edu> 1.5.0-1
- Initial build. I started with the biolinux.org rpm, but broke out
most of the deps and built them seperately.
Index: .cvsignore
===================================================================
RCS file: /cvs/extras/rpms/perl-bioperl/devel/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- .cvsignore 11 Apr 2005 22:47:24 -0000 1.1
+++ .cvsignore 11 Apr 2005 22:50:21 -0000 1.2
@@ -0,0 +1 @@
+bioperl-1.5.0.tar.bz2
Index: sources
===================================================================
RCS file: /cvs/extras/rpms/perl-bioperl/devel/sources,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- sources 11 Apr 2005 22:47:24 -0000 1.1
+++ sources 11 Apr 2005 22:50:21 -0000 1.2
@@ -0,0 +1 @@
+425ac55ecbb4339b7b532ba6d429bb40 bioperl-1.5.0.tar.bz2
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