Initial commit.

(Portage version: 2.1.1_pre5-r2)

5 files changed, 74 insertions, 0 deletions

diff --git a/sci-biology/phyml/ChangeLog b/sci-biology/phyml/ChangeLog
new file mode 100644
index 000000000000..6f83916d7bc2
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+# ChangeLog for sci-biology/phyml
+# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/phyml/ChangeLog,v 1.1 2006/08/18 19:27:04 gongloo Exp $
+
+*phyml-2.4.5 (18 Aug 2006)
+
+  18 Aug 2006; <gongloo@gentoo.org> +metadata.xml, +phyml-2.4.5.ebuild:
+  Initial commit.
+
diff --git a/sci-biology/phyml/Manifest b/sci-biology/phyml/Manifest
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index 000000000000..45461c4003d5
--- /dev/null
+++ b/sci-biology/phyml/Manifest
@@ -0,0 +1,16 @@
+DIST phyml_v2.4.5.tar.gz 92143 RMD160 4883cefd023a59ec6a8e6a780774b1800b37d714 SHA1 d76920654ca50c97fa7db77125ccce29f572d238 SHA256 e8a1d3980137f8e528d0e59472aff37dbac615860a7d3ee4cdb64f30dfea296e
+EBUILD phyml-2.4.5.ebuild 613 RMD160 10b932fb3ca8838d2c4db31b0e7369030ce1256c SHA1 cd5240dc7273d3f00d3a0e28064fdf580c7d039a SHA256 ddb092a97808cae0e39ee64e0c7737923570b3fc9c1dcbcd124cd8c3b1e02979
+MD5 01e0a9a53f63399a9ca8ba07612ad0aa phyml-2.4.5.ebuild 613
+RMD160 10b932fb3ca8838d2c4db31b0e7369030ce1256c phyml-2.4.5.ebuild 613
+SHA256 ddb092a97808cae0e39ee64e0c7737923570b3fc9c1dcbcd124cd8c3b1e02979 phyml-2.4.5.ebuild 613
+MISC ChangeLog 237 RMD160 6ca027c257b49d07a4fea6e3fe97f58fbc5ac252 SHA1 e1d593a67f1c6d5f594506ca9e30205b8c04626e SHA256 a22fe01469587669a7b238aa16cd93dd6882ed05ff8f1280b592807c3cde3447
+MD5 821a00ee90f001354d8aafcdf5d10260 ChangeLog 237
+RMD160 6ca027c257b49d07a4fea6e3fe97f58fbc5ac252 ChangeLog 237
+SHA256 a22fe01469587669a7b238aa16cd93dd6882ed05ff8f1280b592807c3cde3447 ChangeLog 237
+MISC metadata.xml 564 RMD160 dc4cbace6d7f96e731e560aa5314c2de6a9ea4aa SHA1 2aaab7f56a7504822506f038d02dd4c66280e4b4 SHA256 cc398ec9629e0921a5a6cc6a48fb8335b65d50ae688084695be0e7a69b24f3bd
+MD5 41be34e91fd4f20dde9cb012b5599f89 metadata.xml 564
+RMD160 dc4cbace6d7f96e731e560aa5314c2de6a9ea4aa metadata.xml 564
+SHA256 cc398ec9629e0921a5a6cc6a48fb8335b65d50ae688084695be0e7a69b24f3bd metadata.xml 564
+MD5 f859d84d728057f03bda2f75a758456e files/digest-phyml-2.4.5 235
+RMD160 55cb97b716dd7ddd79e14a4b23f865bfdf1ceb29 files/digest-phyml-2.4.5 235
+SHA256 e02e2f7050b7712bd606568cd5fb87c20109e4a44e509708464ecdbd38edb89d files/digest-phyml-2.4.5 235
diff --git a/sci-biology/phyml/files/digest-phyml-2.4.5 b/sci-biology/phyml/files/digest-phyml-2.4.5
new file mode 100644
index 000000000000..8dc8a884bdf1
--- /dev/null
+++ b/sci-biology/phyml/files/digest-phyml-2.4.5
@@ -0,0 +1,3 @@
+MD5 0958e17f973feffb8df2f6616672a075 phyml_v2.4.5.tar.gz 92143
+RMD160 4883cefd023a59ec6a8e6a780774b1800b37d714 phyml_v2.4.5.tar.gz 92143
+SHA256 e8a1d3980137f8e528d0e59472aff37dbac615860a7d3ee4cdb64f30dfea296e phyml_v2.4.5.tar.gz 92143
diff --git a/sci-biology/phyml/metadata.xml b/sci-biology/phyml/metadata.xml
new file mode 100644
index 000000000000..67bf9cb6373d
--- /dev/null
+++ b/sci-biology/phyml/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-biology</herd>
+	<maintainer>
+		<email>gongloo@gentoo.org</email>
+		<name>Hasan Khalil</name>
+	</maintainer>
+	<longdescription lang="en">
+		 Phyml is a simple, fast, and accurate algorithm to estimate large
+		 phylogenies by maximum likelihood. Given input sequence files, it
+		 estimates phylogenies using maximum likelihood, and is capable of
+		 processing large amounts of phylogenetic data.
+	</longdescription>
+</pkgmetadata>
diff --git a/sci-biology/phyml/phyml-2.4.5.ebuild b/sci-biology/phyml/phyml-2.4.5.ebuild
new file mode 100644
index 000000000000..0d67726acd6b
--- /dev/null
+++ b/sci-biology/phyml/phyml-2.4.5.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/phyml/phyml-2.4.5.ebuild,v 1.1 2006/08/18 19:27:04 gongloo Exp $
+
+DESCRIPTION="A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood."
+HOMEPAGE="http://atgc.lirmm.fr/phyml/"
+SRC_URI="http://www.lirmm.fr/~guindon/${PN}_v${PV}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND=""
+
+S=${WORKDIR}/${PN}_v${PV}
+
+src_unpack() {
+	unpack ${A}
+	cd ${S}
+	sed -i -e 's/^hello !!!//' -e 's/^CFLAGS =/#CFLAGS =/' -e 's/^CC =/#CC =/' Makefile
+}
+
+src_compile() {
+	make
+}
+
+src_install() {
+	dobin phyml
+}