reinit the tree, so we can have metadata

4 files changed, 117 insertions, 0 deletions

diff --git a/sci-biology/phyml/Manifest b/sci-biology/phyml/Manifest
new file mode 100644
index 000000000000..ee94a3c2ecce
--- /dev/null
+++ b/sci-biology/phyml/Manifest
@@ -0,0 +1,6 @@
+AUX phyml-2.4.5-fix-build-system.patch 1735 SHA256 0635b908cfb0b5cd58dfe7bffd22c6b5f24e8cca4f0ba077062831377649b0b5 SHA512 95079d00d4a7373f9b6f9b17b707ae999db38a341e03f96b5f1b023ea4fd76a4027f6a46c6e33ecf7902ab4dcbc22d199b5c0f75a7b0059c90f7c11fbc9146cf WHIRLPOOL 63bd683e9d57172a53a2bb65ecca0d781b249d73ae8db092c615524666d00b0cc89a9bec80f7678b1d9883c48d3b0a09c131303377da73cf454ae7c74eca6120
+DIST phyml_v2.4.5.tar.gz 92143 SHA256 e8a1d3980137f8e528d0e59472aff37dbac615860a7d3ee4cdb64f30dfea296e SHA512 119716290eca0de4da05b0bacbec96139f4c89f6a033b861d1cb2655a620766bd0bea0675c4d7722a31d888652a28bf3544a643f39f11682982ede80dc5928c3 WHIRLPOOL e9c0e36ea871c61fc617ed0a10d306bdb66d84da0b9a08107fb9e1f6370e10676c5ad8a0a5e5404ccad6ae2f62551d566614a173cfdd4a0a523f727fc7924ce0
+EBUILD phyml-2.4.5-r3.ebuild 538 SHA256 22bf7f9b8b325d70ff7ee5e63207e2cb94a0fd0b0a2f723c623a7aad6753f090 SHA512 72a9907fa91529e696da775b9b99282c3df09e79d01a793601d949a593c05870ee0086c596fded675c1ef485f2d3a8d618447493ce90a786015a85a3848ec7e7 WHIRLPOOL 3ed65d9bce2c3313f1a08111388ac6c44c328cc9e66ca3237ced0ec07752af63584bba7181886b745a1b0c47c785b3bb859efdd457948f462bdad2aeca0b814f
+MISC ChangeLog 2430 SHA256 d2024494a36343204465656b7b40db70cfcce68862a2ea52217fb2e0fafbee1a SHA512 1154e0a5002833a4be31df6686f0847daa4495af1175544d61928cbf6ce534ccafebbc33eb8946eb7721d1bd1298bf2458f50ac078d355492101f3fc499ea134 WHIRLPOOL fe22e48888de5c18570f7b1deabddfbd2d9949bab745808e294a2965332fce6b451e5b3229c895e3eb3dfcd5410b0af346da00ee363715b46cff42e54c8a972a
+MISC ChangeLog-2015 1617 SHA256 ffa16cf31a589b692e8eeb21f9aebdb4ff68f52c50814178f65c6ebf1f9aab76 SHA512 b30f1127d8e02b6ba3e3860d604fcfc57cad9ef4f633faa20783bab48c54adbd4dbf5c472c43e5204b472574a3966d9aa579e3f0ee1880321ad8ea8c0a610630 WHIRLPOOL 93bfdd0d44b46ae9af184cbdd915c99000691e7395d1a280ec097d333cd11eb0c447b29a693dd42ea32d3c5959310ee8e9306889578f7925c92169ab640f8950
+MISC metadata.xml 574 SHA256 94713e777819ed96a655c5806190e2d62fd824bbd1c9242071505fc31476ba23 SHA512 0f25e0d422671c08446bd97be45b2f00e95cf793666ee6ece0652eeb8e27fd983896e3f865f4e5d7a04231355bbd6047dd19dac0ce3490ec78562305255c1a2b WHIRLPOOL 79885b18e00ff582d6746b0efef1b34901935edd9f4a753751ea846201264652b143418dad2a1a8d950cc52ab456a8fe272616ee2e8aa9c34b142ebc0859d48e
diff --git a/sci-biology/phyml/files/phyml-2.4.5-fix-build-system.patch b/sci-biology/phyml/files/phyml-2.4.5-fix-build-system.patch
new file mode 100644
index 000000000000..9b1d9e03ca14
--- /dev/null
+++ b/sci-biology/phyml/files/phyml-2.4.5-fix-build-system.patch
@@ -0,0 +1,67 @@
+Fix build system to honour user flags.
+
+--- a/Makefile
++++ b/Makefile
+@@ -1,10 +1,4 @@
+-hello !!!
+-
+-CC = gcc #cc
+-CFLAGS = -O4 -fomit-frame-pointer -Wall -static
+-# CFLAGS = -Wall
+-# CFLAGS = -g -Wall
+-# CFLAGS = -pg -Wall -fprofile-arcs -static
++CC ?= gcc
+ LIBS = -lm
+ 
+ PROG = PHYML
+@@ -23,39 +17,39 @@
+ 
+ 
+ $(EXEC) : $(OBJS)
+-	$(CC) -o $(EXEC) $(OBJS) $(LIBS) $(CFLAGS)
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(EXEC) $(OBJS) $(LIBS)
+ 
+ clean :
+ 	@rm *.o
+ ######################################################################################################
+ 
+ eigen.o : eigen.c eigen.h
+-	$(CC) $(CFLAGS) $(DFLAG) -c eigen.c
++	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c eigen.c
+ 
+ simu.o : simu.c simu.h
+-	$(CC) $(CFLAGS) $(DFLAG) -c simu.c
++	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c simu.c
+ 
+ lk.o : lk.c lk.h
+-	$(CC) $(CFLAGS) $(DFLAG) -c lk.c
++	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c lk.c
+ 
+ utilities.o : utilities.c utilities.h
+-	$(CC) $(CFLAGS) $(DFLAG) -c utilities.c
++	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c utilities.c
+ 
+ optimiz.o : optimiz.c optimiz.h
+-	$(CC) $(CFLAGS) $(DFLAG) -c optimiz.c
++	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c optimiz.c
+ 
+ bionj.o : bionj.c bionj.h
+-	$(CC) $(CFLAGS) $(DFLAG) -c bionj.c
++	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c bionj.c
+ 
+ main.o : main.c
+-	$(CC) $(CFLAGS) $(DFLAG) -c main.c
++	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c main.c
+ 
+ models.o : models.c models.h
+-	$(CC) $(CFLAGS) $(DFLAG) -c models.c
++	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c models.c
+ 
+ free.o : free.c free.h
+-	$(CC) $(CFLAGS) $(DFLAG) -c free.c
++	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c free.c
+ 
+ options.o : options.c options.h
+-	$(CC) $(CFLAGS) $(DFLAG) -c options.c
++	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c options.c
+ 
diff --git a/sci-biology/phyml/metadata.xml b/sci-biology/phyml/metadata.xml
new file mode 100644
index 000000000000..68536249891c
--- /dev/null
+++ b/sci-biology/phyml/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <longdescription lang="en">
+		 Phyml is a simple, fast, and accurate algorithm to estimate large
+		 phylogenies by maximum likelihood. Given input sequence files, it
+		 estimates phylogenies using maximum likelihood, and is capable of
+		 processing large amounts of phylogenetic data.
+	</longdescription>
+</pkgmetadata>
diff --git a/sci-biology/phyml/phyml-2.4.5-r3.ebuild b/sci-biology/phyml/phyml-2.4.5-r3.ebuild
new file mode 100644
index 000000000000..098771430632
--- /dev/null
+++ b/sci-biology/phyml/phyml-2.4.5-r3.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs
+
+MY_P=${PN}_v${PV}
+
+DESCRIPTION="Estimation of large phylogenies by maximum likelihood"
+HOMEPAGE="http://atgc.lirmm.fr/phyml/"
+SRC_URI="http://www.lirmm.fr/~guindon/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="amd64 ppc x86"
+IUSE=""
+
+S=${WORKDIR}/${MY_P}
+
+PATCHES=( "${FILESDIR}"/${PN}-2.4.5-fix-build-system.patch )
+
+src_prepare() {
+	default
+	tc-export CC
+}
+
+src_install() {
+	dobin phyml
+}