proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

5 files changed, 105 insertions, 0 deletions

diff --git a/sci-biology/readseq/Manifest b/sci-biology/readseq/Manifest
new file mode 100644
index 000000000000..bcd1dfa237bf
--- /dev/null
+++ b/sci-biology/readseq/Manifest
@@ -0,0 +1,2 @@
+DIST readseq-20100513.zip 628406 SHA256 878b689828bdf59a73c377c314fe504b9f18569ed5cd512acdb264cf90e72601 SHA512 6e2a2207e3a1f14e5cc4f7ffd2c74563b6deb088dda02727611359a17e1b157d9c661715d1f896d1573786cb88f61d3b952ab7a53e6dc30f2dcbcead58604b32 WHIRLPOOL 6f5b7ff075a081f521971689d014ad3ea6ffdc50db1b24766712d21fb86f83d7767f9afa76473f0be6f36560c8572c7051337cde8020cb9562dfef96a2bfdc8a
+DIST readseq-source-20080420.zip 627341 SHA256 d91ccadcbf5fde29525c639ece6ae132e0db863a7e63f96f69647e591617e8dd SHA512 cbc7afa46d2f0cfb30aa75ab88e4942a18ddf46a03a4cfb8d7e07bd23bce3fe015483899d371b947a0f1d6ec464b8c1238df7f7fc89753bb75dbb284f1e07b48 WHIRLPOOL fb180c53cb0555887d5278871498d66840d1d27da47ef6a947f0cd048bfb79762faf9493a645be6909bf41c5627131f3ced8d29b8241372d1e6034dc7524004d
diff --git a/sci-biology/readseq/files/20080420-no-bundling.patch b/sci-biology/readseq/files/20080420-no-bundling.patch
new file mode 100644
index 000000000000..f2e1708f8821
--- /dev/null
+++ b/sci-biology/readseq/files/20080420-no-bundling.patch
@@ -0,0 +1,14 @@
+diff --git a/build.xml b/build.xml
+index e3d723c..4b44d6f 100644
+--- a/build.xml
++++ b/build.xml
+@@ -229,9 +229,6 @@
+ 
+     <!-- for now, unjar xml classes into build/classes and rejar in readseq.jar -->
+     
+-    <unjar overwrite="false" src="${orgxml.jar}" dest="${build.home}/classes" />
+-    <unjar overwrite="false" src="${xml.jar}" dest="${build.home}/classes" />
+-    
+ <!--      <copy todir="${build.home}/classes""> -->
+ <!--       <src dir="${basedir}/META-INF"/> -->
+ <!--     </copy> -->
diff --git a/sci-biology/readseq/metadata.xml b/sci-biology/readseq/metadata.xml
new file mode 100644
index 000000000000..b198f044f3f5
--- /dev/null
+++ b/sci-biology/readseq/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <longdescription>
+		Reads and writes nucleic/protein sequences in various formats. Data
+		files may have multiple sequences.
+	</longdescription>
+</pkgmetadata>
diff --git a/sci-biology/readseq/readseq-20080420-r1.ebuild b/sci-biology/readseq/readseq-20080420-r1.ebuild
new file mode 100644
index 000000000000..43c538beb596
--- /dev/null
+++ b/sci-biology/readseq/readseq-20080420-r1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit java-pkg-2 java-ant-2
+
+MY_P="${PN}-source-${PV}"
+DESCRIPTION="Reads and writes nucleic/protein sequences in various formats"
+HOMEPAGE="http://iubio.bio.indiana.edu/soft/molbio/readseq/"
+# Originally unversioned at
+# http://iubio.bio.indiana.edu/soft/molbio/readseq/java/readseq-source.zip.
+# Renamed to the date of the modification and mirrored
+SRC_URI="http://dev.gentoo.org/~dberkholz/distfiles/${MY_P}.zip"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="!=sci-biology/meme-4.8.1
+	>=virtual/jre-1.4"
+DEPEND=">=virtual/jdk-1.4
+	app-arch/unzip"
+
+S=${WORKDIR}
+
+java_prepare() {
+	rm "${S}"/lib/* || die
+	epatch "${FILESDIR}"/${PV}-*
+}
+
+src_install() {
+	java-pkg_dojar build/readseq.jar
+	java-pkg_dolauncher
+}
+
+pkg_postinst() {
+	elog "Documentation is available at"
+	elog "http://iubio.bio.indiana.edu/soft/molbio/readseq/java/Readseq2-help.html"
+}
diff --git a/sci-biology/readseq/readseq-20100513.ebuild b/sci-biology/readseq/readseq-20100513.ebuild
new file mode 100644
index 000000000000..6539ebd427cc
--- /dev/null
+++ b/sci-biology/readseq/readseq-20100513.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Reads and writes nucleic/protein sequences in various formats"
+HOMEPAGE="http://iubio.bio.indiana.edu/soft/molbio/readseq/"
+SRC_URI="http://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.zip"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="!=sci-biology/meme-4.8.1
+	>=virtual/jre-1.4"
+DEPEND=">=virtual/jdk-1.4
+	app-arch/unzip"
+
+S=${WORKDIR}
+
+java_prepare() {
+	rm "${S}"/lib/* || die
+	epatch "${FILESDIR}"/20080420-*
+}
+
+src_install() {
+	java-pkg_dojar build/readseq.jar
+	java-pkg_dolauncher
+}
+
+pkg_postinst() {
+	elog "Documentation is available at"
+	elog "http://iubio.bio.indiana.edu/soft/molbio/readseq/java/Readseq2-help.html"
+}