reinit the tree, so we can have metadata

4 files changed, 79 insertions, 0 deletions

diff --git a/sci-biology/sim4/Manifest b/sci-biology/sim4/Manifest
new file mode 100644
index 000000000000..ff74c4d56e58
--- /dev/null
+++ b/sci-biology/sim4/Manifest
@@ -0,0 +1,6 @@
+AUX sim4-20030921-fix-build-system.patch 491 SHA256 f61c6bd531fa66de77e60a3eb0fcd1fbf0050900909be6b3b8e6f7e6ae06e327 SHA512 fdc737ccacd7cb4f7c5534af49587d7958f62dbe66a5197c38bda89af3cdd572231c10af75e8bb59120fa116f856f1ca5ba95279f9a2fe07228543588552f915 WHIRLPOOL 2b519969382729ce1aa2585a54bea390141e01c2df7b040b788e42b33ce5a4a97864ff0dd11b47f6786d217fece9a90928049f3eb2a55656ef6652d92e297cd9
+DIST sim4.tar.gz 60814 SHA256 0d65166c1d1951e1d0b83e5d221f23f07462b9d8c46ea0d0569f66e35a5229ee SHA512 de7ee4094830262cb7ea8ed2f4573beed96df4b12f2915f669c52fd3fa40f5a4894cd94224e575bfb2588f9a6f19c0b73a38d6209d92a1dc644639a4927aa6b5 WHIRLPOOL b8d7cbcf44a03b5b13a51204e424e7e6ac2ab862e942c943b2a2f0d50bd1a823e3c1542fb2033f4b13f1539a636fb582c8d63b6406e2dc774f72f3eea7cc8004
+EBUILD sim4-20030921-r2.ebuild 553 SHA256 7eea5ed01863028a6640e75be0482c7efbe5e3b7bd39621715fc1a2e9865f997 SHA512 51fd5d759f62b005bc33b2fc37dbf8dc3f8b993d461d5dc2722ed93f8a8e51c19d21ea82105c3544ed23ad831c7e2d5c86e5c63aa3aa19937c4c354426e37f71 WHIRLPOOL 4267cbf1885b56d86cf96fd2bdedbb7f2ecd92c7eb8e3e03edbb15b87411b4d9f0197340d3426ab5dde6bbba84f679bfc9bf664fba6d7fc76eeef48b7e9e0241
+MISC ChangeLog 2485 SHA256 6270458054b23d23137856ecb7ebb2d48cb2f4f19de504de7399a4e42af6f85d SHA512 fd61ae1d8f5f27088860e8ff6c04e82de1b9beb08fa310882ff7839cbe7dad838d974f3f6a3875bd8a700cb6b4d3b7a9a375ba309777634503f614a4e948ac49 WHIRLPOOL d79ee3e790e820ddedc080e8649477620dae5b9263f76c1e1c105b11c2ec5603a724ecea6794e3b02d87d0dd5f696b1c8a57c222cc2f2fafd8402ab938c27d39
+MISC ChangeLog-2015 1401 SHA256 c43bba4aab69e4b6a96a907a221c706459b726c3e84460c91bfab41799995425 SHA512 ba70237e17cfdc2ca0553f0ebfd8f72d43ed5f28b5d8b89ea70a6e9d16155da0ff4e29e52519782fe635451fb266551afce9436c0d174a204d480faa8a5eccab WHIRLPOOL aa0b1744d2e31c31f555240c21e107b5f17b2709a485088e91a3e44e52b3433d54e4a6e47d7d2c2cb1ac29541c6f53ced275e41f33df216e794da432178e2a11
+MISC metadata.xml 1228 SHA256 f3afc9dceef2eb3ee4ad39648b3478a165c1ac0299e3b91a8fb9f8defccb9597 SHA512 417eff4c0d22bb4bef9bd027c79171375f9638e7efd452444d2c2a40b79a02c24f69b6158448420970a86e87358ed6bd397307b227cbe1b3bbf6813b6433d565 WHIRLPOOL 8d44044f8c3326919e7dc10b6d875dd9a6e6f549f8c47a223dff0bf0219eb0b307825be7415a88d02fac64c42a31bc552331ead417fa783db019b792acb32694
diff --git a/sci-biology/sim4/files/sim4-20030921-fix-build-system.patch b/sci-biology/sim4/files/sim4-20030921-fix-build-system.patch
new file mode 100644
index 000000000000..8fd50fe9cfae
--- /dev/null
+++ b/sci-biology/sim4/files/sim4-20030921-fix-build-system.patch
@@ -0,0 +1,21 @@
+Fix build system to honour user flags.
+
+--- a/Makefile
++++ b/Makefile
+@@ -1,13 +1,11 @@
+-
+ # For better performance, replace ``-O'' with whatever
+ # the best optimization flag is for your computer.
+ # For Sun's compilers under Solaris, ``-fast'' works well.
+ # For gcc, ``-O2'' works well.
+-CC=cc
+-CFLAGS=-O
+-LDLIBS=-lm
++CC ?= gcc
++LDLIBS = -lm
+  
+ sim4:
+-	$(CC) -o sim4 -I. $(CFLAGS) *.c $(LDLIBS)
++	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o sim4 -I. *.c $(LDLIBS)
+ clean:
+ 	rm -f sim4 *.o
diff --git a/sci-biology/sim4/metadata.xml b/sci-biology/sim4/metadata.xml
new file mode 100644
index 000000000000..6366d6fb797e
--- /dev/null
+++ b/sci-biology/sim4/metadata.xml
@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<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-r2.ebuild b/sci-biology/sim4/sim4-20030921-r2.ebuild
new file mode 100644
index 000000000000..204ec82210ae
--- /dev/null
+++ b/sci-biology/sim4/sim4-20030921-r2.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+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}/${PN}.2003-09-21
+
+PATCHES=( "${FILESDIR}"/${PN}-20030921-fix-build-system.patch )
+
+src_configure() {
+	tc-export CC
+}
+
+src_install() {
+	dobin ${PN}
+	einstalldocs
+}