From 70cef6f6adab5a8f429a0bdc92ccb5eb5bbe1453 Mon Sep 17 00:00:00 2001 From: Stephen Diener Date: Sat, 25 Oct 2003 02:19:58 +0000 Subject: new ebuild and associated files for 1.2.3 --- app-sci/bioperl/Manifest | 5 +- app-sci/bioperl/bioperl-1.2.3.ebuild | 76 ++++++++++++++++++ app-sci/bioperl/files/biodbgff-enable-1.2.3.patch | 98 +++++++++++++++++++++++ app-sci/bioperl/files/digest-bioperl-1.2.3 | 1 + 4 files changed, 177 insertions(+), 3 deletions(-) create mode 100644 app-sci/bioperl/bioperl-1.2.3.ebuild create mode 100644 app-sci/bioperl/files/biodbgff-enable-1.2.3.patch create mode 100644 app-sci/bioperl/files/digest-bioperl-1.2.3 (limited to 'app-sci') diff --git a/app-sci/bioperl/Manifest b/app-sci/bioperl/Manifest index 67e6a66e70eb..4ce856a295fe 100644 --- a/app-sci/bioperl/Manifest +++ b/app-sci/bioperl/Manifest @@ -1,10 +1,9 @@ -MD5 d6c0f860388ca0e549be025fae20e759 ChangeLog 1109 +MD5 695c557a2d99a16f01020e407d49ee67 ChangeLog 1109 MD5 20616984167d7ac1a9db33713d70e93f bioperl-1.0.2.ebuild 1496 MD5 ce01843f37edf576d07e2423ee6d486e bioperl-1.2.ebuild 1524 MD5 683bbc29b2f9f4f309efbecfea7184a1 bioperl-1.2.2.ebuild 2198 MD5 e8b4df3df76800c376905734d8043cfa metadata.xml 216 -MD5 f568ff8b7d8eb751c6ba2087cfdd4b1e bioperl-1.2.3.ebuild 2082 -MD5 97abac8473042e6aaaad6ac8a9f66fb8 .bioperl-1.2.3.ebuild.swp 12288 +MD5 07780e6c7f94982c8a22e55fea7383fb bioperl-1.2.3.ebuild 2082 MD5 1828ff2ba6225e17a98d27bfbad5c7c9 files/bioperl-1.2-manpage.diff 712 MD5 dfdb9921cbef92f60e9746a9531d8de7 files/digest-bioperl-1.0.2 66 MD5 14b9e16331895fe40e231065f7dda942 files/digest-bioperl-1.2 64 diff --git a/app-sci/bioperl/bioperl-1.2.3.ebuild b/app-sci/bioperl/bioperl-1.2.3.ebuild new file mode 100644 index 000000000000..27ffc8201d59 --- /dev/null +++ b/app-sci/bioperl/bioperl-1.2.3.ebuild @@ -0,0 +1,76 @@ +# Copyright 1999-2003 Gentoo Technologies, Inc. +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/app-sci/bioperl/bioperl-1.2.3.ebuild,v 1.1 2003/10/25 02:19:54 sediener Exp $ + +inherit perl-module eutils +CATEGORY="app-sci" + +DESCRIPTION="collection of tools for bioinformatics, genomics and life science research" +HOMEPAGE="http://www.bioperl.org/" +#SRC_URI="http://www.cpan.org/modules/by-module/Bio/${P}.tar.gz" +SRC_URI="http://www.bioperl.org/ftp/DIST/${P}.tar.bz2" + +LICENSE="Artistic GPL-2" +SLOT="0" +KEYWORDS="x86" +IUSE="mysql gd" + +DEPEND="${DEPEND} + dev-perl/File-Temp + dev-perl/HTML-Parser + dev-perl/IO-String + dev-perl/IO-stringy + dev-perl/SOAP-Lite + dev-perl/Storable + dev-perl/XML-DOM + dev-perl/XML-Parser + dev-perl/XML-Writer + dev-perl/XML-Twig + dev-perl/libxml-perl + dev-perl/libwww-perl + dev-perl/Graph + dev-perl/Text-Shellwords + gd? ( >=dev-perl/GD-1.32-r1 ) + mysql? ( >=dev-perl/DBD-mysql-2.1004-r3 )" + +src_unpack() { + unpack ${A} + cd ${S} + # remove interactiveness + [ -n "`use mysql`" ] && epatch ${FILESDIR}/biodbgff-enable-${PV}.patch + # want man pages in addition to perldoc documentation?? + #epatch ${FILESDIR}/domanpages-${PV}.patch +} + +src_compile() { + # there's a test to run for BioGFFDB if using mysql + perl-module_src_compile || die "compile failed" + # make test +## perl-module_src_test || die "src test failed" +} + +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install + + # bioperl scripts and examples + einfo 'Adding bioperl examples and scripts to /usr/share/...' + dodir /usr/share/${PF}/scripts + cd ${S}/scripts/ + tar cf - ./ | ( cd ${D}/usr/share/${PF}/scripts; tar xf -) + dodir /usr/share/${PF}/examples + cd ${S}/examples/ + tar cf - ./ | ( cd ${D}/usr/share/${PF}/examples; tar xf -) + dodir /usr/share/doc/${P} + cd ${S} + tar cf - ./ | ( cd ${D}/usr/share/doc/${P}; tar xf -) + + # some pods in maindir + eval `perl '-V:installvendorlib'` + MY_SITE_LIB=${installvendorlib}/Bio + insinto ${MY_SITE_LIB} + doins biodatabases.pod biodesign.pod bioperl.pod bioscripts.pod + + dobin bptutorial.pl + +} diff --git a/app-sci/bioperl/files/biodbgff-enable-1.2.3.patch b/app-sci/bioperl/files/biodbgff-enable-1.2.3.patch new file mode 100644 index 000000000000..7bd66206a0b4 --- /dev/null +++ b/app-sci/bioperl/files/biodbgff-enable-1.2.3.patch @@ -0,0 +1,98 @@ +--- Makefile.PL.orig 2003-07-14 16:09:49.000000000 +0100 ++++ Makefile.PL 2003-07-14 16:15:56.000000000 +0100 +@@ -83,9 +83,6 @@ + # Prompt user for BioDBGFF stuff + # + +-if( eval { require DBI } && grep {/mysql/} DBI->available_drivers) { +- my $proceed = prompt("Do you want to run the BioDBGFF tests (requires a mysql database) y/n",'n'); +- if( $proceed =~ /^[yY]/) { + my $cfg = {dbd_driver => 'mysql'}; + GFFQueryDb($cfg,{'prompt'=>1,'verbose'=>1}); + if (open T,">t/do_biodbgff.tests") { +@@ -94,13 +91,6 @@ + } + close T; + } +- } else { +- if( -e "t/do_biodbgff.tests" ) { +- unlink "t/do_biodbgff.tests"; +- } +- } +-} +- + + ############################################################################ + # +@@ -124,55 +114,27 @@ + my $d = lc $driver; + my $prompt = $options->{'prompt'}; + +- my $test_db = exists($options->{"$d-test-db"}) ? +- $options->{"$d-test-db"} : ($cfg->{'test_db'} || 'test'); +- $test_db = prompt +- ("Which database should I use for testing the $db drivers?", +- $test_db) if $prompt; +- +- my $test_host = exists($options->{"$d-test-host"}) ? +- $options->{"$d-test-host"} : ($cfg->{'test_host'} || 'localhost'); +- $test_host = prompt +- ("On which host is database $test_db running (hostname, ip address or host:port)", $test_host) if $prompt; +- +- my($test_user, $test_pass); +- +- $test_user = exists($options->{"$d-test-user"}) ? +- $options->{"$d-test-user"} : ($cfg->{'test_user'} || "undef"); +- $test_user = prompt +- ("User name for connecting to database $test_db?", $test_user) +- if $prompt; +- $test_user = undef if $test_user eq 'undef'; +- +- $test_pass = exists($options->{"$d-test-pass"}) ? +- $options->{"$d-test-pass"} : ($cfg->{'test_pass'} || "undef"); +- $test_pass = prompt +- ("Password for connecting to database $test_db?", $test_pass) +- if $prompt; +- $test_pass = undef if $test_pass eq 'undef'; +- +- $cfg->{'test_db'} = $test_db; +- $cfg->{'test_host'} = $test_host; +- $cfg->{'test_user'} = $test_user; +- $cfg->{'test_pass'} = $test_pass; +- if ($test_host eq 'undef' || $test_host eq 'localhost') { +- $test_host = ''; +- } +- my $test_dsn = "DBI:$driver:database=$test_db"; +- $cfg->{test_dsn} = $test_dsn; +- if ($test_host) { +- $cfg->{'test_dsn'} .= ";host=$test_host"; +- } ++ $options->{"$d-test-db"} = 'test'; ++ $options->{"$d-test-host"} = 'localhost'; ++ $options->{"$d-test-user"} = n0b0dy; ++ $options->{"$d-test-pass"} = undef; ++ ++ $cfg->{'test_db'} = $options->{"$d-test-db"}; ++ $cfg->{'test_host'} = $options->{"$d-test-host"}; ++ $cfg->{'test_user'} = $options->{"$d-test-user"}; ++ $cfg->{'test_pass'} = $options->{"$d-test-pass"}; + ++ my $test_dsn = "DBI:$driver:database=" . $cfg->{test_db}; ++ $cfg->{'test_dsn'} = $test_dsn; + + if ($options->{'verbose'}) { + local $^W=0; # some uninitialized variable warning coming through + print("Driver $driver is using the following settings for tests:\n", +- " Database $test_db\n", +- " Host $test_host\n", +- " DSN $test_dsn\n", +- " User $test_user\n", +- " Password $test_pass\n"); ++ " Database ".$cfg->{test_db}. "\n", ++ " Host ".$cfg->{test_host}."\n", ++ " DSN ".$cfg->{test_dsn}. "\n", ++ " User ".$cfg->{test_user}."\n", ++ " Password ".$cfg->{test_pass}."\n"); + } + } + diff --git a/app-sci/bioperl/files/digest-bioperl-1.2.3 b/app-sci/bioperl/files/digest-bioperl-1.2.3 new file mode 100644 index 000000000000..05b4fc161597 --- /dev/null +++ b/app-sci/bioperl/files/digest-bioperl-1.2.3 @@ -0,0 +1 @@ +MD5 c64219b6540a722e781a53aea215ebc8 bioperl-1.2.3.tar.bz2 3086024 -- cgit v1.2.3-65-gdbad