From: Olivier Fisette <ribosome@gentoo.org>
Date: Thu, 23 Dec 2004 22:11:24 +0000 (+0000)
Subject: Moving to sci-biology/bioperl-pipeline
X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=a78cc0c0688a87b1b561b386d96871072038720b;p=gentoo.git

Moving to sci-biology/bioperl-pipeline
---

diff --git a/app-sci/bioperl-pipeline/ChangeLog b/app-sci/bioperl-pipeline/ChangeLog
deleted file mode 100644
index e5549424d9c6..000000000000
--- a/app-sci/bioperl-pipeline/ChangeLog
+++ /dev/null
@@ -1,21 +0,0 @@
-# ChangeLog for app-sci/bioperl-pipeline
-# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/bioperl-pipeline/ChangeLog,v 1.5 2004/08/03 11:48:24 dholm Exp $
-
-  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/app-sci/bioperl-pipeline/Manifest b/app-sci/bioperl-pipeline/Manifest
deleted file mode 100644
index 7dfd7b17d39c..000000000000
--- a/app-sci/bioperl-pipeline/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-MD5 affc5f5c241ac93e24743dcb4a204eed bioperl-pipeline-0.1.ebuild 1962
-MD5 bda4eecce29fd270dedec6fd130d2d49 ChangeLog 703
-MD5 e8b4df3df76800c376905734d8043cfa metadata.xml 216
-MD5 cea8881ae00a651493915c7732732233 files/digest-bioperl-pipeline-0.1 72
diff --git a/app-sci/bioperl-pipeline/bioperl-pipeline-0.1.ebuild b/app-sci/bioperl-pipeline/bioperl-pipeline-0.1.ebuild
deleted file mode 100644
index 02fd41799a49..000000000000
--- a/app-sci/bioperl-pipeline/bioperl-pipeline-0.1.ebuild
+++ /dev/null
@@ -1,73 +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-pipeline/bioperl-pipeline-0.1.ebuild,v 1.9 2004/12/23 22:10:42 ribosome Exp $
-
-inherit perl-module
-CATEGORY="app-sci"
-
-DESCRIPTION="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_unpack() {
-	unpack ${A}
-	cd ${S}
-}
-
-src_compile() {
-	# there's a test to run for BioGFFDB if using mysql
-	perl-module_src_compile || die "compile failed"
-	# make test
-	##	perl-module_src_test || die "src test failed"
-	ewarn " "
-	ewarn "Tests skipped since they will fail unless"
-	ewarn "mysql root user has no password"
-	ewarn " "
-}
-
-src_install() {
-	mydoc="AUTHORS README LICENSE INSTALL FAQ database_schema.doc database_tables.txt"
-	perl-module_src_install
-
-	# bioperl scripts and examples
-	einfo "Adding bioperl-pipeline scripts, sql and xml directories to /usr/share/${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/app-sci/bioperl-pipeline/files/digest-bioperl-pipeline-0.1 b/app-sci/bioperl-pipeline/files/digest-bioperl-pipeline-0.1
deleted file mode 100644
index a489d75fab99..000000000000
--- a/app-sci/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/app-sci/bioperl-pipeline/metadata.xml b/app-sci/bioperl-pipeline/metadata.xml
deleted file mode 100644
index 8a4bcd47220d..000000000000
--- a/app-sci/bioperl-pipeline/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>