Moving to sci-biology/bioperl-run

diff --git a/app-sci/bioperl-run/ChangeLog b/app-sci/bioperl-run/ChangeLog
deleted file mode 100644 (file)
index 317f54a..0000000
--- a/app-sci/bioperl-run/ChangeLog
+++ /dev/null
@@ -1,28 +0,0 @@
-# ChangeLog for app-sci/bioperl-run
-# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/bioperl-run/ChangeLog,v 1.7 2004/09/23 19:48:15 sediener Exp $
-
-  23 Sep 2004; Stephen Diener <sediener@gentoo.org> bioperl-run-1.4.ebuild:
-  Bumped 1.4 to stable on x86
-
-  03 Aug 2004; David Holm <dholm@gentoo.org> bioperl-run-1.4.ebuild:
-  Added to ~ppc.
-
-  22 Mar 2004; Patrick Kursawe <phosphan@gentoo.org> bioperl-run-1.2.2.ebuild,
-  bioperl-run-1.4.ebuild:
-  removing DEPEND="${RDEPEND}"
-
-*bioperl-run-1.4 (08 Jan 2004)
-
-  08 Jan 2004; Stephen Diener <sediener@gentoo.org> bioperl-run-1.4.ebuild:
-  version bump to 1.4
-
-  14 Dec 2003; Stephen Diener <sediener@gentoo.org> bioperl-run-1.2.2.ebuild:
-  Bump to stable
-
-*bioperl-run-1.2.2 (29 Sep 2003)
-
-  29 Sep 2003; <sediener@gentoo.org> bioperl-run-1.2.2.ebuild, metadata.xml,
-  files/bioperl-run-Pise-test-patch.diff:
-  Initial Import. Built of of the bioperl ebuild from Gontran Zepeda.
-

diff --git a/app-sci/bioperl-run/Manifest b/app-sci/bioperl-run/Manifest
deleted file mode 100644 (file)
index 20d30ca..0000000
--- a/app-sci/bioperl-run/Manifest
+++ /dev/null
@@ -1,7 +0,0 @@
-MD5 4cd3241aa707d6a6d276fd13d119e7d6 bioperl-run-1.4.ebuild 1306
-MD5 5c2ee510b374b6726d8b226c24662a5c bioperl-run-1.2.2.ebuild 1456
-MD5 81eb9eddaa9c418106d796b152b14ed0 ChangeLog 995
-MD5 e8b4df3df76800c376905734d8043cfa metadata.xml 216
-MD5 47db6a1f839dd45f8c891b5f6ab2ff2a files/digest-bioperl-run-1.4 67
-MD5 21ad123058f1e670f289ee1a87de4e82 files/bioperl-run-Pise-test-patch.diff 722
-MD5 b23d441d6d3f1d4ed3dead4c3dc2799b files/digest-bioperl-run-1.2.2 69

diff --git a/app-sci/bioperl-run/bioperl-run-1.2.2.ebuild b/app-sci/bioperl-run/bioperl-run-1.2.2.ebuild
deleted file mode 100644 (file)
index e229d3d..0000000
--- a/app-sci/bioperl-run/bioperl-run-1.2.2.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2004 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/bioperl-run/bioperl-run-1.2.2.ebuild,v 1.4 2004/06/24 21:52:54 agriffis Exp $
-
-inherit perl-module eutils
-CATEGORY="app-sci"
-
-DESCRIPTION="collection of tools for bioinformatics, genomics and life science research : subset required to run analyses"
-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.gz"
-
-LICENSE="Artistic GPL-2"
-SLOT="0"
-KEYWORDS="x86"
-IUSE=""
-
-RDEPEND="
-       dev-perl/Algorithm-Diff
-       dev-perl/File-Temp
-       dev-perl/IO-String
-       dev-perl/XML-Parser"
-
-DEPEND=""
-
-src_unpack() {
-       unpack ${A}
-       cd ${S}
-       # remove interactiveness
-       epatch ${FILESDIR}/bioperl-run-Pise-test-patch.diff
-}
-
-src_compile() {
-       # there's a test to run for BioGFFDB if using mysql
-       perl-module_src_compile || die "compile failed"
-       # make test
-##     perl-module_src_test || die "src test failed"
-}
-
-src_install() {
-       mydoc="AUTHORS BUGS FAQ"
-       perl-module_src_install
-
-       # bioperl scripts and examples
-       einfo 'Adding bioperl examples and scripts to /usr/share/...'
-       dodir /usr/share/${PF}/scripts
-       #insinto /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 -)
-       cd ${S}
-
-}

diff --git a/app-sci/bioperl-run/bioperl-run-1.4.ebuild b/app-sci/bioperl-run/bioperl-run-1.4.ebuild
deleted file mode 100644 (file)
index a0a217c..0000000
--- a/app-sci/bioperl-run/bioperl-run-1.4.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2004 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/bioperl-run/bioperl-run-1.4.ebuild,v 1.5 2004/09/23 19:48:15 sediener Exp $
-
-inherit perl-module eutils
-CATEGORY="app-sci"
-
-DESCRIPTION="collection of tools for bioinformatics, genomics and life science research : subset required to run analyses"
-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.gz"
-
-LICENSE="Artistic GPL-2"
-SLOT="0"
-KEYWORDS="x86 ~ppc"
-IUSE=""
-
-RDEPEND="
-       dev-perl/Algorithm-Diff
-       dev-perl/File-Temp
-       dev-perl/IO-String
-       dev-perl/XML-Parser"
-
-DEPEND=""
-
-src_compile() {
-       perl-module_src_compile || die "compile failed"
-       # make test
-       #perl-module_src_test || die "src test failed"
-}
-
-src_install() {
-       mydoc="AUTHORS BUGS INSTALL.PROGRAMS README"
-       perl-module_src_install
-
-       # bioperl scripts and examples
-       einfo 'Adding bioperl examples and scripts to /usr/share/...'
-       dodir /usr/share/${PF}/scripts
-       #insinto /usr/share/${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 -)
-       cd ${S}
-
-}

diff --git a/app-sci/bioperl-run/files/bioperl-run-Pise-test-patch.diff b/app-sci/bioperl-run/files/bioperl-run-Pise-test-patch.diff
deleted file mode 100644 (file)
index 5683347..0000000
--- a/app-sci/bioperl-run/files/bioperl-run-Pise-test-patch.diff
+++ /dev/null
@@ -1,22 +0,0 @@
---- Makefile.PL.original       2003-09-28 23:33:16.000000000 -0400
-+++ Makefile.PL        2003-09-28 23:33:50.000000000 -0400
-@@ -73,19 +73,6 @@
- my $DISTNAME = "bioperl-run";
- my $VERSION  = "1.2.2";
- 
--my $proceed = prompt("Do you want to run the Pise tests (requires a network connection) y/n",'n');
--if( $proceed =~ /^[yY]/) {
--    my $address = prompt("Enter your email address (no default)",'');
--   
--    if (open T,">t/pise-email.test") {
--print T "$address\n";
--close T;
--    } else { warn("Cannot open file t/pise-email.test for writing - no Pise tests will be run"); }
--} else {
--    if( -e "t/pise-email.test" ) {
--unlink "t/pise-email.test";
--    }
--}
- #$do_autoload_finesse = 0;
- #$NAME     = 'Bio';
- #$DISTNAME = "GFD";

diff --git a/app-sci/bioperl-run/files/digest-bioperl-run-1.2.2 b/app-sci/bioperl-run/files/digest-bioperl-run-1.2.2
deleted file mode 100644 (file)
index cf92f27..0000000
--- a/app-sci/bioperl-run/files/digest-bioperl-run-1.2.2
+++ /dev/null
@@ -1 +0,0 @@
-MD5 2ffbaa69e713f102f86c7b7462ccff52 bioperl-run-1.2.2.tar.gz 811989

diff --git a/app-sci/bioperl-run/files/digest-bioperl-run-1.4 b/app-sci/bioperl-run/files/digest-bioperl-run-1.4
deleted file mode 100644 (file)
index 5c20ece..0000000
--- a/app-sci/bioperl-run/files/digest-bioperl-run-1.4
+++ /dev/null
@@ -1 +0,0 @@
-MD5 25914ab48d1ab0393ebb067a8f68a821 bioperl-run-1.4.tar.gz 830774

diff --git a/app-sci/bioperl-run/metadata.xml b/app-sci/bioperl-run/metadata.xml
deleted file mode 100644 (file)
index 8a4bcd4..0000000
--- a/app-sci/bioperl-run/metadata.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci</herd>
-<maintainer><email>sediener@gentoo.org</email></maintainer>
-</pkgmetadata>