Removing sci-biology/bioperl-pipeline. Upstream is dead, bioperl has evolved beyond.

5 files changed, 0 insertions, 126 deletions

diff --git a/sci-biology/bioperl-pipeline/ChangeLog b/sci-biology/bioperl-pipeline/ChangeLog
deleted file mode 100644
index c06b722530e7..000000000000
--- a/sci-biology/bioperl-pipeline/ChangeLog
+++ /dev/null
@@ -1,33 +0,0 @@
-# ChangeLog for sci-biology/bioperl-pipeline
-# Copyright 2000-2005 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-pipeline/ChangeLog,v 1.4 2005/11/28 12:01:43 mcummings Exp $
-
-  28 Nov 2005; <mcumming@gentoo.org> bioperl-pipeline-0.1.ebuild:
-  Switched from perl-module to perl-app eclass
-
-  19 Sep 2005; Olivier Fisette <ribosome@gentoo.org> metadata.xml:
-  Maintainer changed from Stephen Diener (MIA) to Olivier Fisette.
-
-*bioperl-pipeline-0.1 (23 Dec 2004)
-
-  23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
-  +bioperl-pipeline-0.1.ebuild:
-  Moved from app-sci/bioperl-pipeline to sci-biology/bioperl-pipeline.
-
-  03 Aug 2004; David Holm <dholm@gentoo.org> bioperl-pipeline-0.1.ebuild:
-  Added to ~ppc.
-
-  22 Mar 2004; Patrick Kursawe <phosphan@gentoo.org>
-  bioperl-pipeline-0.1.ebuild:
-  Removing DEPEND="${RDEPEND}"
-
-  15 Dec 2003; Stephen Diener <sediener@gentoo.org>
-  bioperl-pipeline-0.1.ebuild:
-  Added missing dependency ncbi-tools
-
-*bioperl-pipeline-0.1 (15 Dec 2003)
-
-  15 Dec 2003; Stephen Diener <sediener@gentoo.org>
-  bioperl-pipeline-0.1.ebuild:
-  New ebuild -- initial release
-
diff --git a/sci-biology/bioperl-pipeline/Manifest b/sci-biology/bioperl-pipeline/Manifest
deleted file mode 100644
index 088fd9c73c36..000000000000
--- a/sci-biology/bioperl-pipeline/Manifest
+++ /dev/null
@@ -1,16 +0,0 @@
-DIST bioperl-pipeline-0.1.tar.gz 633893
-EBUILD bioperl-pipeline-0.1.ebuild 1887 RMD160 aeabf508435936b90b82130caf3a0372bad31fca SHA1 22ad317764c7c7a796017b2e8d27d03561780786 SHA256 20c4cb17d9b06970642b7889a575d12f1de2b52bdcadc80c13af6eb523e7ab94
-MD5 24a000aef0648f0ad640f965156951cf bioperl-pipeline-0.1.ebuild 1887
-RMD160 aeabf508435936b90b82130caf3a0372bad31fca bioperl-pipeline-0.1.ebuild 1887
-SHA256 20c4cb17d9b06970642b7889a575d12f1de2b52bdcadc80c13af6eb523e7ab94 bioperl-pipeline-0.1.ebuild 1887
-MISC ChangeLog 1173 RMD160 5535ed5b2e47dfbe3ada3e0a2a0cb7d90171ecf7 SHA1 04e3a68a283c8a133e05b74ea1ef27af5a88c9af SHA256 692949f246e07657342b47e342dd77db8498d80eb2a9380871e86a741bfd4f4d
-MD5 7e35f9d2609cd8c9877930cd8752a4f5 ChangeLog 1173
-RMD160 5535ed5b2e47dfbe3ada3e0a2a0cb7d90171ecf7 ChangeLog 1173
-SHA256 692949f246e07657342b47e342dd77db8498d80eb2a9380871e86a741bfd4f4d ChangeLog 1173
-MISC metadata.xml 262 RMD160 4eabcbcb990d4d5e3b34db8c27bcd2c0cfcf7501 SHA1 3c024ca60a2b93ed0e0311f6b05ef5ef117bee31 SHA256 89af818a993faf14a4a87e2f254943420156c2a317c385480a9533ba682b650f
-MD5 5f35ae4b4cb1cd144db7c7c093d3fd80 metadata.xml 262
-RMD160 4eabcbcb990d4d5e3b34db8c27bcd2c0cfcf7501 metadata.xml 262
-SHA256 89af818a993faf14a4a87e2f254943420156c2a317c385480a9533ba682b650f metadata.xml 262
-MD5 cea8881ae00a651493915c7732732233 files/digest-bioperl-pipeline-0.1 72
-RMD160 c740221870f99234b294fbecfc49a4bc1067a2ea files/digest-bioperl-pipeline-0.1 72
-SHA256 1c0f43ce92ccecd8b5461f539ad95d9a70e48dc22b035f588d7465775acdf340 files/digest-bioperl-pipeline-0.1 72
diff --git a/sci-biology/bioperl-pipeline/bioperl-pipeline-0.1.ebuild b/sci-biology/bioperl-pipeline/bioperl-pipeline-0.1.ebuild
deleted file mode 100644
index b675fcb20e93..000000000000
--- a/sci-biology/bioperl-pipeline/bioperl-pipeline-0.1.ebuild
+++ /dev/null
@@ -1,67 +0,0 @@
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-pipeline/bioperl-pipeline-0.1.ebuild,v 1.6 2005/11/28 12:01:43 mcummings Exp $
-
-inherit perl-app
-
-DESCRIPTION="A collection of tools for bioinformatics, genomics and life science research: Biopipe"
-HOMEPAGE="http://www.biopipe.org/"
-SRC_URI="mirror://gentoo/$P.tar.gz"
-
-LICENSE="Artistic GPL-2"
-SLOT="0"
-KEYWORDS="~x86 ~ppc"
-IUSE=""
-
-RDEPEND="
-	dev-db/mysql
-	>=sci-biology/ncbi-tools-20031103
-	>=sci-biology/bioperl-1.2.3
-	>=sci-biology/bioperl-run-1.2.2
-	dev-perl/XML-SimpleObject
-	dev-perl/XML-Parser
-	dev-perl/Data-ShowTable"
-
-DEPEND=""
-
-src_compile() {
-	# there's a test to run for BioGFFDB if using mysql
-	perl-module_src_compile || die "compile failed"
-	# make test
-	##	perl-module_src_test || die "src test failed"
-	ewarn
-	ewarn "Tests skipped since they will fail unless"
-	ewarn "mysql root user has no password"
-	ewarn
-}
-
-src_install() {
-	mydoc="AUTHORS README LICENSE INSTALL FAQ database_schema.doc database_tables.txt"
-	perl-module_src_install
-
-	# bioperl scripts and examples
-	einfo "Adding bioperl-pipeline scripts, sql and xml directories to /usr/share/${PF}..."
-	dodir /usr/share/${PF}/scripts
-	cd ${S}/scripts/
-	tar cf - ./ | ( cd ${D}/usr/share/${PF}/scripts; tar xf -)
-	dodir /usr/share/${PF}/sql
-	cd ${S}/sql/
-	tar cf - ./ | ( cd ${D}/usr/share/${PF}/sql; tar xf -)
-	dodir /usr/share/${PF}/xml
-	cd ${S}/xml/
-	tar cf - ./ | ( cd ${D}/usr/share/${PF}/xml; tar xf -)
-	dodir /usr/share/doc/${PF}/
-	cd ${S}/doc/
-	tar cf - ./ | ( cd ${D}/usr/share/doc/${PF}; tar xf -)
-	cd ${S}
-
-}
-
-pkg_postinst() {
-	einfo
-	einfo "You will need to modify Bio/Pipeline/PipeConf.pm"
-	einfo "with mysql user and batch job software information"
-	einfo "Read the docs in /usr/share/docs/${PF}"
-	einfo "for more information"
-	einfo
-}
diff --git a/sci-biology/bioperl-pipeline/files/digest-bioperl-pipeline-0.1 b/sci-biology/bioperl-pipeline/files/digest-bioperl-pipeline-0.1
deleted file mode 100644
index a489d75fab99..000000000000
--- a/sci-biology/bioperl-pipeline/files/digest-bioperl-pipeline-0.1
+++ /dev/null
@@ -1 +0,0 @@
-MD5 91cd12769a4e22889a2c508c290a8965 bioperl-pipeline-0.1.tar.gz 633893
diff --git a/sci-biology/bioperl-pipeline/metadata.xml b/sci-biology/bioperl-pipeline/metadata.xml
deleted file mode 100644
index ebbff811d3b4..000000000000
--- a/sci-biology/bioperl-pipeline/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer>
-		<email>ribosome@gentoo.org</email>
-		<name>Olivier Fisette</name>
-	</maintainer>
-	<herd>sci-biology</herd>
-</pkgmetadata>