commit: 48c3969c6bbd4c14e06285180baf5ca376114835 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Fri May 24 08:44:39 2024 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Fri May 24 08:44:39 2024 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=48c3969c
sci-biology/raxml: add 8.2.13 Bug: https://bugs.gentoo.org/822408 Bug: https://bugs.gentoo.org/831489 Signed-off-by: David Seifert <soap <AT> gentoo.org> sci-biology/raxml/Manifest | 1 + .../raxml/files/raxml-8.2.13-makefile.patch | 37 +++++++++++++++++++++ sci-biology/raxml/metadata.xml | 11 ++++--- sci-biology/raxml/raxml-8.2.13.ebuild | 38 ++++++++++++++++++++++ 4 files changed, 83 insertions(+), 4 deletions(-) diff --git a/sci-biology/raxml/Manifest b/sci-biology/raxml/Manifest index 8b5ec91eee6e..648666691355 100644 --- a/sci-biology/raxml/Manifest +++ b/sci-biology/raxml/Manifest @@ -1 +1,2 @@ DIST RAxML-7.2.6.tar.bz2 202803 BLAKE2B 579676ff9fad1563eabb9507015acff010977a89ae087df9b828b80bc9352ed44c98faeaf4c8d884ffa14176bfa28772dc9872ad8b5d401aff8b834c728e5f65 SHA512 b0027a7e583e6471a774d9e784a0be1ff63b3824a8cfbebca68bf9e414adab297206ea2d43c9b97456e6acc0a6a15f55ca33983381dd6150f9e7ea71ddecdcd3 +DIST raxml-8.2.13.tar.gz 10201721 BLAKE2B ee48dc599947619d12a54cafef1eee554abc0df30a31ba2fdb501b228dadec9f137acff8f472047f4686304f74d27893696c95ff808baa128c2c3d83539366a1 SHA512 c99dc3f8c8798cda38c644501f474c0261e72c1f3b64d594d5006fa03e8d8c4da3bdf20b8e3c6c9f669c9509d5af27a0c286a2570a54c8ff7df7cd63c1f78885 diff --git a/sci-biology/raxml/files/raxml-8.2.13-makefile.patch b/sci-biology/raxml/files/raxml-8.2.13-makefile.patch new file mode 100644 index 000000000000..d774b1fb824d --- /dev/null +++ b/sci-biology/raxml/files/raxml-8.2.13-makefile.patch @@ -0,0 +1,37 @@ +--- a/Makefile.gcc ++++ b/Makefile.gcc +@@ -1,7 +1,6 @@ + # Makefile August 2006 by Alexandros Stamatakis + # Makefile cleanup October 2006, Courtesy of Peter Cordes <pe...@cordes.ca> + +-CC = gcc + + ARCH := $(shell uname -m) + ifeq ($(ARCH), x86_64) +@@ -10,7 +9,7 @@ + ARCH_CFLAGS= + endif + +-CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 $(ARCH_CFLAGS) #-Wall -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast ++CFLAGS += -D_GNU_SOURCE #-Wall -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast + + LIBRARIES = -lm + +@@ -23,7 +22,7 @@ + GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h + + raxmlHPC : $(objs) +- $(CC) -o raxmlHPC $(objs) $(LIBRARIES) $(LDFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES) + + rmqs.o : rmqs.c $(GLOBAL_DEPS) + classify.o : classify.c $(GLOBAL_DEPS) +@@ -51,8 +50,6 @@ + + + +-eigen.o : eigen.c $(GLOBAL_DEPS) +- $(CC) -c -o eigen.o eigen.c + clean : + $(RM) *.o raxmlHPC + diff --git a/sci-biology/raxml/metadata.xml b/sci-biology/raxml/metadata.xml index ccdff086e20b..dd68d972db31 100644 --- a/sci-biology/raxml/metadata.xml +++ b/sci-biology/raxml/metadata.xml @@ -1,8 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd";> <pkgmetadata> - <maintainer type="project"> - <email>sci-biol...@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> + <maintainer type="project"> + <email>sci-biol...@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="github">stamatak/standard-RAxML</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/raxml/raxml-8.2.13.ebuild b/sci-biology/raxml/raxml-8.2.13.ebuild new file mode 100644 index 000000000000..859016195389 --- /dev/null +++ b/sci-biology/raxml/raxml-8.2.13.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit flag-o-matic toolchain-funcs + +DESCRIPTION="Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees" +HOMEPAGE="https://github.com/stamatak/standard-RAxML"; +SRC_URI="https://github.com/stamatak/standard-RAxML/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/standard-RAxML-${PV}" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="cpu_flags_x86_sse3 +threads" + +# mpi is not supported in version 7.2.2. mpi is enabled by adding -DPARALLEL to CFLAGS +PATCHES=( "${FILESDIR}"/${P}-makefile.patch ) + +src_configure() { + use cpu_flags_x86_sse3 && + append-cppflags -D__SIM_SSE3 && + append-cflags -msse3 + use threads && + append-cppflags -D_USE_PTHREADS && + append-cflags -pthread + + tc-export CC +} + +src_compile() { + emake -f Makefile.gcc +} + +src_install() { + dobin raxmlHPC +}
