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- update bioperl to 1.6.1

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This commit is contained in:
jasper 2010-12-16 12:05:04 +00:00
parent 1782b7cee7
commit 5752992555
11 changed files with 1180 additions and 264 deletions
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40
biology/bioperl/Makefile
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@ -1,10 +1,9 @@
# $OpenBSD: Makefile,v 1.8 2010/12/13 10:26:00 jasper Exp $
# $OpenBSD: Makefile,v 1.9 2010/12/16 12:05:04 jasper Exp $
COMMENT= perl tools for bioinformatics
DISTNAME= bioperl-1.5.0
PKGNAME= ${DISTNAME} # No p5-prefix here.
REVISION= 1
DISTNAME= BioPerl-1.6.1
PKGNAME= ${DISTNAME:L} # No p5-prefix here.
CATEGORIES= biology
HOMEPAGE= http://bioperl.org/
@ -21,38 +20,47 @@ MODULES= cpan
MODCPAN_EXAMPLES= Yes
MODCPAN_EXAMPLES_DIR= ${PREFIX}/share/examples/bioperl/
CONFIGURE_STYLE=modbuild
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= biology/AcePerl \
databases/p5-DBD-mysql \
converters/p5-Convert-Binary-C \
devel/p5-Array-Compare \
devel/p5-Class-AutoClass \
devel/p5-Clone \
devel/p5-Data-Stag \
devel/p5-Graph \
devel/p5-IO-String \
devel/p5-IO-stringy \
devel/p5-Set-Scalar \
devel/p5-Test-Exception \
devel/p5-Tree-DAG_Node \
graphics/p5-GD \
graphics/p5-GD-SVG \
graphics/p5-SVG \
graphics/p5-SVG-Graph \
math/p5-GraphViz \
textproc/p5-XML-DOM \
textproc/p5-Libxml \
textproc/p5-XML-Parser \
textproc/p5-XML-SAX \
textproc/p5-XML-SAX-Writer \
textproc/p5-XML-Simple \
textproc/p5-XML-Twig \
textproc/p5-XML-Writer \
www/p5-HTML-Parser \
www/p5-SOAP-Lite \
www/p5-URI \
www/p5-libwww
REGRESS_DEPENDS=${RUN_DEPENDS}
# stuff not yet integrated:
# SVG::Graph, Generate optional SVG output,
# (The Bio::TreeIO::svggraph in Bioperl needs it for creating SVG images)
# XML::SAX::Writer, New style SAX parser,
# (The Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax in Bioperl needs it for Writers)
# srsperl, Sequence Retrieval System (SRS) perl
# (needed for API/alternative way of retrieving sequences/Bio::LiveSeq::IO::SRS.pm)
# Optional (not ported) dependencies:
# Algorithm-Munkres
# Postscript-TextBlock
# Spreadsheet-ParseExcel
# Tie-Cacher
# XML-Dom-XPath
CONFIGURE_ENV+= PERL_MM_USE_DEFAULT=Yes
pre-configure:
@rm -f ${WRKSRC}/Bio/Graphics/FeatureFile.pm.orig
.include <bsd.port.mk>

10
biology/bioperl/distinfo
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@ -1,5 +1,5 @@
MD5 (bioperl-1.5.0.tar.gz) = FyRy8Gdd6aWDQy4hybG1/A==
RMD160 (bioperl-1.5.0.tar.gz) = ErMn6/EJyE5e9RmQ7YRJuuS2FB4=
SHA1 (bioperl-1.5.0.tar.gz) = tVzmHV2kS8AwcwebwaWjgyScyN8=
SHA256 (bioperl-1.5.0.tar.gz) = 835t4S38x7FI0Z2mo/VgkWzufFzNSYN4rlVHMyX+vOo=
SIZE (bioperl-1.5.0.tar.gz) = 6000924
MD5 (BioPerl-1.6.1.tar.gz) = qojxIsEHFP0nvupLcLZZrQ==
RMD160 (BioPerl-1.6.1.tar.gz) = Rq6CqFSllUhVD/vltpHb7KwbXvU=
SHA1 (BioPerl-1.6.1.tar.gz) = vwjsr6roLCDg4ywTQAUGTpnKQmY=
SHA256 (BioPerl-1.6.1.tar.gz) = rDbazitN2XNWewLM4pFYvqwF/WcocsqHaeArvd3claM=
SIZE (BioPerl-1.6.1.tar.gz) = 10462526

12
biology/bioperl/patches/patch-Bio_Graphics_FeatureFile_pm
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@ -1,12 +0,0 @@
$OpenBSD: patch-Bio_Graphics_FeatureFile_pm,v 1.1.1.1 2005/03/03 01:42:12 espie Exp $
--- Bio/Graphics/FeatureFile.pm.orig Thu Mar 3 01:16:54 2005
+++ Bio/Graphics/FeatureFile.pm Thu Mar 3 01:17:17 2005
@@ -120,7 +120,7 @@ use Bio::DB::GFF::Util::Rearrange;
use Carp;
use Bio::DB::GFF;
use IO::File;
-use Text::Shellwords;
+use Text::ParseWords;
# default colors for unconfigured features
my @COLORS = qw(cyan blue red yellow green wheat turquoise orange);

12
biology/bioperl/patches/patch-INSTALL
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@ -1,12 +0,0 @@
$OpenBSD: patch-INSTALL,v 1.1.1.1 2005/03/03 01:42:12 espie Exp $
--- INSTALL.orig Thu Mar 3 01:16:54 2005
+++ INSTALL Thu Mar 3 01:17:40 2005
@@ -485,7 +485,7 @@ o DEPENDENCIES AND Bundle::BioPerl
Storable Persistent object storage & retrieval
Bio::DB::FileCache
- Text::Shellwords Text parser
+ Text::ParseWords Text parser
Bio::Graphics::FeatureFile
XML::DOM XML parser

12
biology/bioperl/patches/patch-Makefile_PL
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@ -1,12 +0,0 @@
$OpenBSD: patch-Makefile_PL,v 1.1.1.1 2005/03/03 01:42:12 espie Exp $
--- Makefile.PL.orig Thu Mar 3 01:16:54 2005
+++ Makefile.PL Thu Mar 3 01:17:04 2005
@@ -29,7 +29,7 @@
'HTML::Parser' => '0.0/HTML parsing/HTML parsing of GDB page/Bio::DB::GDB',
'DBD::mysql' => '0.0/Mysql driver/loading and querying of Mysql-based GFF feature databases/Bio::DB::GFF',
'GD' => '1.3/Graphical Drawing Toolkit/rendering Sequences and Features/Bio::Graphics',
- 'Text::Shellwords' => '0.0/Execute shell commands/test scripts/Bio::Graphics',
+ 'Text::ParseWords' => '0.0/Execute shell commands/test scripts/Bio::Graphics',
'SVG' => '2.26/Generate optional SVG output/Bio::Graphics/Bio::Graphics::Pictogram',
'SVG::Graph' => '0.01/Generate optional SVG output/creating SVG images/Bio::TreeIO::svggraph',
'GD::SVG' => '0.0/Generate optional SVG output/creating SVG images/Bio::Graphics::Panel',

21
biology/bioperl/patches/patch-doc_howto_html_Graphics-HOWTO_html
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@ -1,21 +0,0 @@
$OpenBSD: patch-doc_howto_html_Graphics-HOWTO_html,v 1.1.1.1 2005/03/03 01:42:12 espie Exp $
--- doc/howto/html/Graphics-HOWTO.html.orig Thu Mar 3 01:16:54 2005
+++ doc/howto/html/Graphics-HOWTO.html Thu Mar 3 01:18:04 2005
@@ -77,9 +77,7 @@ BioPerl DocBook
around). If you use libgd 2.0.1 or higher, be sure it matches GD
version 2.0.1 or higher.
</p><p>
- You will also need to install the Text::Shellwords module, which is
- available from CPAN.
- </p></div><div class="section" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a id="gettingStarted"></a>3.&nbsp;Getting Started</h2></div></div><div></div></div><p>
+ </div><div class="section" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a id="gettingStarted"></a>3.&nbsp;Getting Started</h2></div></div><div></div></div><p>
All the code examples and BLAST input files we'll use are available in
the doc/howto/examples/graphics directory in the BioPerl package.
</p><p>
@@ -865,4 +863,4 @@ PRES1 127 310 700
"perldoc Bio::Graphics::Glyph::arrow."
</p></div></div></div><div xmlns="" id="customfooter">
BioPerl DocBook
-</div></body></html>
\ No newline at end of file
+</div></body></html>

14
biology/bioperl/patches/patch-doc_howto_sgml_Graphics-HOWTO_xml
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@ -1,14 +0,0 @@
$OpenBSD: patch-doc_howto_sgml_Graphics-HOWTO_xml,v 1.1.1.1 2005/03/03 01:42:12 espie Exp $
--- doc/howto/sgml/Graphics-HOWTO.xml.orig Thu Mar 3 01:16:54 2005
+++ doc/howto/sgml/Graphics-HOWTO.xml Thu Mar 3 01:18:17 2005
@@ -149,10 +149,6 @@
version 2.0.1 or higher.
</para>
- <para>
- You will also need to install the Text::Shellwords module, which is
- available from CPAN.
- </para>
</section>
<section id="gettingStarted">

13
biology/bioperl/patches/patch-doc_howto_txt_Graphics-HOWTO_txt
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@ -1,13 +0,0 @@
$OpenBSD: patch-doc_howto_txt_Graphics-HOWTO_txt,v 1.1.1.1 2005/03/03 01:42:12 espie Exp $
--- doc/howto/txt/Graphics-HOWTO.txt.orig Thu Mar 3 01:16:54 2005
+++ doc/howto/txt/Graphics-HOWTO.txt Thu Mar 3 01:18:21 2005
@@ -95,9 +95,6 @@ Lincoln Stein
around). If you use libgd 2.0.1 or higher, be sure it matches GD
version 2.0.1 or higher.
- You will also need to install the Text::Shellwords module, which is
- available from CPAN.
-
3. Getting Started
All the code examples and BLAST input files we'll use are available in

18
biology/bioperl/patches/patch-t_BioGraphics_t
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@ -1,18 +0,0 @@
$OpenBSD: patch-t_BioGraphics_t,v 1.1.1.1 2005/03/03 01:42:12 espie Exp $
--- t/BioGraphics.t.orig Thu Mar 3 01:16:54 2005
+++ t/BioGraphics.t Thu Mar 3 01:17:24 2005
@@ -32,12 +32,12 @@ BEGIN {
eval {
require GD;
- require Text::Shellwords;
+ require Text::ParseWords;
require Bio::Graphics::FeatureFile;
require Bio::Graphics;
};
if( $@ ) {
- print STDERR "GD or Text::Shellwords modules are not installed. This means that Bio::Graphics module is unusable. Skipping tests.\n";
+ print STDERR "GD or Text::ParseWords modules are not installed. This means that Bio::Graphics module is unusable. Skipping tests.\n";
$error = 1;
}
}

3
biology/bioperl/pkg/DESCR
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@ -1 +1,2 @@
Bioperl is a package of Perl tools for computational molecular biology.
BioPerl is a toolkit of perl modules useful in building bioinformatics
solutions in Perl.

1289
biology/bioperl/pkg/PLIST
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