reinit the tree, so we can have metadata

3 files changed, 60 insertions, 0 deletions

diff --git a/sci-biology/paml/Manifest b/sci-biology/paml/Manifest
new file mode 100644
index 000000000000..d91078ef56e8
--- /dev/null
+++ b/sci-biology/paml/Manifest
@@ -0,0 +1,5 @@
+DIST paml4.4c.tar.gz 2891715 SHA256 08aad25b6b06a359d4f2f12a60ea601c95694864d5f29f7028f67b80890974d6 SHA512 6a5f6d5baa91afa924ea392b76e59db6691fa9d6ee13a248dfe6e46d3fc83178ce41c2991de1c4cdb21952ee53771298aa0c62060f47d0dd84eaa76eb533498a WHIRLPOOL 44ae42dd6088039be1041cdce70ce9ee907b8f85d4e25f9d556df4738ea3ea91f700f96f627f20a13d226038132fd23aecbc5b452bfb6716b9499c8d2be491e4
+EBUILD paml-4.4c-r1.ebuild 983 SHA256 b26af56a27830d61800dcde4748c7bf8e22e7bdcc5bf64ca699fadc7bc202cfa SHA512 a7d590056e148c08607c6c15e872f6fc4ea87166336f19eeef497efb4852481b782b83f8e40b6f50005dffaa45b1fb6d028cd101fd54efa643e3678e60836b04 WHIRLPOOL 06bcfe96dc03e4e7a53973485fe857326543d3f0cfaddc69b82100d7afacd3cfa0d46cfbbf296fc34c03e160f8d332daed07fae8e9b4333620b4b04aed1f4568
+MISC ChangeLog 2425 SHA256 d403a8cfba0398d18886db184fe791caaeca0a0491f2d071f83786aa12fe8d05 SHA512 8906f03dc75d0a5b1e986df0a1f67d3a7eadcb7faeed673e20744d5df93d01f6703cae009e329cebc11798d3d8a4310174106dcd3928915ebaf36e76444de534 WHIRLPOOL 0f080599fbecf90cd407a61052c36b20679e633f967539fd6acde91b5fb803e5a9773d890bae96c3436d0d8f1ffdaa9c4c055d1606b7412212400a360b9da4c4
+MISC ChangeLog-2015 2630 SHA256 6c2d59aeba797855630a7d38aaae91f36b31d2b2a48e71a7798d89901a3bffe6 SHA512 baed8489c9c2684a208f9f42096a299d268048ea19a0c71e43bc4f17a9f8438f14ab702c31bb4c252bddd6452469fa7641ba6694a7899d22ab9ee2f02df8f8eb WHIRLPOOL 19701038e949a640bedf1caada118ec3272591c45f215c66c0c355fcc5445086f925a7e8e4060064a822ecdec75ad8c4d4765499aaaeda8b25670c9b801febf1
+MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13
diff --git a/sci-biology/paml/metadata.xml b/sci-biology/paml/metadata.xml
new file mode 100644
index 000000000000..959160fe46b1
--- /dev/null
+++ b/sci-biology/paml/metadata.xml
@@ -0,0 +1,8 @@
+<?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>
+</pkgmetadata>
diff --git a/sci-biology/paml/paml-4.4c-r1.ebuild b/sci-biology/paml/paml-4.4c-r1.ebuild
new file mode 100644
index 000000000000..27fe5ed4c769
--- /dev/null
+++ b/sci-biology/paml/paml-4.4c-r1.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit toolchain-funcs versionator
+
+MY_P=$(version_format_string '${PN}$1$2')
+
+DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood"
+HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html"
+SRC_URI="http://abacus.gene.ucl.ac.uk/software/${PN}${PV}.tar.gz"
+
+LICENSE="free-noncomm"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE=""
+
+S=${WORKDIR}/${MY_P}
+
+src_prepare() {
+	# Notice send by mail to prof. Ziheng Yang
+	sed -i "s/\$(CC)/& \$(LDFLAGS)/" src/Makefile || die #335608
+}
+
+src_compile() {
+	emake -C src \
+		CC="$(tc-getCC)" \
+		CFLAGS="${CFLAGS} -Wno-unused-result" \
+		LDFLAGS="${LDFLAGS}"
+}
+
+src_install() {
+	dodoc README.txt doc/*
+
+	insinto /usr/share/${PN}/control
+	doins *.ctl
+
+	insinto /usr/share/${PN}/dat
+	doins stewart* *.dat dat/*
+
+	insinto /usr/share/${PN}
+	doins -r examples/
+
+	cd src || die
+	dobin baseml codeml basemlg mcmctree pamp evolver yn00 chi2
+}