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

4 files changed, 67 insertions, 0 deletions

diff --git a/sci-biology/sim4/Manifest b/sci-biology/sim4/Manifest
new file mode 100644
index 000000000000..f2a25200b895
--- /dev/null
+++ b/sci-biology/sim4/Manifest
@@ -0,0 +1 @@
+DIST sim4.tar.gz 60814 RMD160 5acad71daa94893025a21b73b416dd3903078be5 SHA1 11a9170ea03990268d409056084415d725c6290b SHA256 0d65166c1d1951e1d0b83e5d221f23f07462b9d8c46ea0d0569f66e35a5229ee
diff --git a/sci-biology/sim4/metadata.xml b/sci-biology/sim4/metadata.xml
new file mode 100644
index 000000000000..ea9731279003
--- /dev/null
+++ b/sci-biology/sim4/metadata.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-biology</herd>
+	<longdescription>
+		sim4 is a similarity-based tool for aligning an expressed DNA sequence
+		(EST, cDNA, mRNA) with a genomic sequence for the gene. It also detects
+		end matches when the two input sequences overlap at one end (i.e., the
+		start of one sequence overlaps the end of the other).sim4 employs a
+		blast-based technique to first determine the basic matching blocks
+		representing the "exon cores". In this first stage, it detects all
+		possible exact matches of W-mers (i.e., DNA words of size W) between
+		the two sequences and extends them to maximal scoring gap-free
+		segments. In the second stage, the exon cores are extended into the
+		adjacent as-yet-unmatched fragments using greedy alignment algorithms,
+		and heuristics are used to favor configurations that conform to the
+		splice-site recognition signals (GT-AG, CT-AC). If necessary, the
+		process is repeated with less stringent parameters on the unmatched
+		fragments.
+	</longdescription>
+</pkgmetadata>
diff --git a/sci-biology/sim4/sim4-20030921-r1.ebuild b/sci-biology/sim4/sim4-20030921-r1.ebuild
new file mode 100644
index 000000000000..178bf92ab5da
--- /dev/null
+++ b/sci-biology/sim4/sim4-20030921-r1.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+inherit toolchain-funcs
+
+DESCRIPTION="A program to align cDNA and genomic DNA"
+HOMEPAGE="http://globin.cse.psu.edu/html/docs/sim4.html"
+SRC_URI="http://globin.cse.psu.edu/ftp/dist/sim4/sim4.tar.gz"
+LICENSE="GPL-2"
+
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE=""
+
+S=${WORKDIR}/${PN}.2003-09-21
+
+src_compile() {
+	echo "$(tc-getCC) -o ${PN} ${LDFLAGS} -I. ${CFLAGS} *.c -lm"
+	$(tc-getCC) -o ${PN} ${LDFLAGS} -I. ${CFLAGS} *.c -lm || die
+}
+
+src_install() {
+	dobin ${PN} || die
+	dodoc README.* VERSION || die
+}
diff --git a/sci-biology/sim4/sim4-20030921.ebuild b/sci-biology/sim4/sim4-20030921.ebuild
new file mode 100644
index 000000000000..12d5231aa120
--- /dev/null
+++ b/sci-biology/sim4/sim4-20030921.ebuild
@@ -0,0 +1,19 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+DESCRIPTION="A program to align cDNA and genomic DNA"
+HOMEPAGE="http://globin.cse.psu.edu/html/docs/sim4.html"
+SRC_URI="http://globin.cse.psu.edu/ftp/dist/sim4/sim4.tar.gz"
+LICENSE="GPL-2"
+
+SLOT="0"
+KEYWORDS="x86 ~ppc"
+IUSE=""
+
+S="${WORKDIR}/${PN}.2003-09-21"
+
+src_install() {
+	dobin sim4 || die
+	dodoc README.psublast README.sim4 VERSION || die
+}