From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-biology/phyml/Manifest | 6 ++ .../phyml/files/phyml-2.4.5-fix-build-system.patch | 67 ++++++++++++++++++++++ sci-biology/phyml/metadata.xml | 14 +++++ sci-biology/phyml/phyml-2.4.5-r3.ebuild | 30 ++++++++++ 4 files changed, 117 insertions(+) create mode 100644 sci-biology/phyml/Manifest create mode 100644 sci-biology/phyml/files/phyml-2.4.5-fix-build-system.patch create mode 100644 sci-biology/phyml/metadata.xml create mode 100644 sci-biology/phyml/phyml-2.4.5-r3.ebuild (limited to 'sci-biology/phyml') 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) $(CPPFLAGS) -c options.c + diff --git a/sci-biology/phyml/metadata.xml b/sci-biology/phyml/metadata.xml new file mode 100644 index 000000000000..68536249891c --- /dev/null +++ b/sci-biology/phyml/metadata.xml @@ -0,0 +1,14 @@ + + + + + sci-biology@gentoo.org + Gentoo Biology Project + + + Phyml is a simple, fast, and accurate algorithm to estimate large + phylogenies by maximum likelihood. Given input sequence files, it + estimates phylogenies using maximum likelihood, and is capable of + processing large amounts of phylogenetic data. + + diff --git a/sci-biology/phyml/phyml-2.4.5-r3.ebuild b/sci-biology/phyml/phyml-2.4.5-r3.ebuild new file mode 100644 index 000000000000..098771430632 --- /dev/null +++ b/sci-biology/phyml/phyml-2.4.5-r3.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +MY_P=${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 +} -- cgit v1.2.3