reinit the tree, so we can have metadata

4 files changed, 85 insertions, 0 deletions

diff --git a/sci-biology/raxml/Manifest b/sci-biology/raxml/Manifest
new file mode 100644
index 000000000000..4b6ea77c10ad
--- /dev/null
+++ b/sci-biology/raxml/Manifest
@@ -0,0 +1,6 @@
+AUX raxml-7.2.6-makefile.patch 777 SHA256 0e87b5cd6375669e660ef6e3c37e51e751ea8846de6c52060f484380c28610d5 SHA512 0cc326e8fed0882c56193fef9d1c98577f2252acc4dc25e650e0806d89ded0e2911e6967272a6d101cf830cfe63a190a8f5220fd7573864f5fa60106069ad74f WHIRLPOOL 896bb8f27d458e1d555ffb462abf89f55c487e595a604b3446c579a2e95719cfdfb1911873ca2570a73c3299ef49f0c489ee0c127fcb6e1acdcf907c748459b0
+DIST RAxML-7.2.6.tar.bz2 202803 SHA256 d45bcbe45e3ed5f8d6ba3c99b9da9b202c72a9fb196a9d32d2961ee4cb791868 SHA512 b0027a7e583e6471a774d9e784a0be1ff63b3824a8cfbebca68bf9e414adab297206ea2d43c9b97456e6acc0a6a15f55ca33983381dd6150f9e7ea71ddecdcd3 WHIRLPOOL 7fe7ac66412c979d3ecca17e2c06a32566fefe7bdcf39664a0885fcdebc2b8187c222ca5e29cf2685085fba21a8aff0a2aefceec08823cab155a5f62f8b59490
+EBUILD raxml-7.2.6.ebuild 962 SHA256 e23a9d95f88de3f012243d97a65d77cd7ab833933434461293b1622b68805315 SHA512 dd75e9c82ef3a3d2c3c2813690af6ac95548842e727c7819b63054d7e982b4ea7ebfd9020c4ee7b9f80bd0b38162c5559e25a19bf5a60efd2d63e3798fae243b WHIRLPOOL 9ed05cccb01a217e74781d86fd26feebb79ea1dd5045af85c244ffe88e4b788db7703af0fb0921f3613788383138aa0c89ee246dcc2f3ac0517273c553ea3ab3
+MISC ChangeLog 2496 SHA256 3ff7f51068eae5a3ee5aac56ba24c804e27f6532686a11dc4e12dad54105ca39 SHA512 4ae95033b82f5bbbbb89759053c076181d590a50c80f94d09d4854ddbad7c8f35b56b80fc983865fdfdac7c994b54c141b973d1547c32c75f01bfe8c59aa2628 WHIRLPOOL 8b8cd0213bb17cb2c19dfeb5e3dcc76cc9d7fe9fb1be88e6553b7f209de125d18cd7e846c6b751f56b738dfd5d32bfab42d3aceafa08d13f5863c96c91d4c065
+MISC ChangeLog-2015 1843 SHA256 8e1b22930f67ae96d7d4600fcd18797548ef8fe68ac0b4a652691878517897dc SHA512 40d0f7f536b7d7fb6395fdfd443f2e960b42923145d281c5198f3dd86f3fe5afb4eb85f044be8c3222e1728ff691cb34a2684fd7b3c78f36dec0056ded4c5797 WHIRLPOOL dab6051c307797ea0d57bd74d468ef98630070c8c2b51c221437cbf568c8018abc1b567d72fc27c22c7496e8a6e419c9edd5fef7af5009374619fa5068f6c875
+MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13
diff --git a/sci-biology/raxml/files/raxml-7.2.6-makefile.patch b/sci-biology/raxml/files/raxml-7.2.6-makefile.patch
new file mode 100644
index 000000000000..ae83e2eef4e7
--- /dev/null
+++ b/sci-biology/raxml/files/raxml-7.2.6-makefile.patch
@@ -0,0 +1,29 @@
+ Makefile.gcc |    6 +++---
+ 1 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/Makefile.gcc b/Makefile.gcc
+index 716b6c6..f0c1de2 100644
+--- a/Makefile.gcc
++++ b/Makefile.gcc
+@@ -1,10 +1,10 @@
+ # Makefile August 2006 by Alexandros Stamatakis
+ # Makefile cleanup October 2006, Courtesy of Peter Cordes <peter@cordes.ca>
+ 
+-CC = gcc 
++CC ?= gcc 
+ 
+ 
+-CFLAGS = -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse
++CFLAGS += -D_GNU_SOURCE
+ 
+ 
+ 
+@@ -19,7 +19,7 @@ all : raxmlHPC
+ GLOBAL_DEPS = axml.h globalVariables.h
+ 
+ raxmlHPC : $(objs)
+-	$(CC) -o raxmlHPC $(objs) $(LIBRARIES) 
++	$(CC) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES) 
+ 
+ classify.o : classify.c $(GLOBAL_DEPS)
+ evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
diff --git a/sci-biology/raxml/metadata.xml b/sci-biology/raxml/metadata.xml
new file mode 100644
index 000000000000..959160fe46b1
--- /dev/null
+++ b/sci-biology/raxml/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/raxml/raxml-7.2.6.ebuild b/sci-biology/raxml/raxml-7.2.6.ebuild
new file mode 100644
index 000000000000..50fffc34accb
--- /dev/null
+++ b/sci-biology/raxml/raxml-7.2.6.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit eutils flag-o-matic toolchain-funcs
+
+DESCRIPTION="Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees"
+HOMEPAGE="http://wwwkramer.in.tum.de/exelixis/software.html"
+SRC_URI="http://wwwkramer.in.tum.de/exelixis/software/RAxML-${PV}.tar.bz2"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86"
+IUSE="cpu_flags_x86_sse3 +threads"
+
+REQUIRED_USE="cpu_flags_x86_sse3"
+
+# mpi is not supported in version 7.2.2. mpi is enabled by adding -DPARALLEL to CFLAGS
+DEPEND="" # mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/RAxML-${PV}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-makefile.patch
+
+	use cpu_flags_x86_sse3 && append-cflags -D__SIM_SSE3
+	use threads && \
+		append-cflags -D_USE_PTHREADS && \
+		append-ldflags -pthread
+
+	tc-export CC
+}
+
+src_compile() {
+	emake -f Makefile.gcc
+}
+
+src_install() {
+	dobin raxmlHPC
+}