diff options
Diffstat (limited to 'sci-biology/raxml')
| -rw-r--r-- | sci-biology/raxml/Manifest | 8 | ||||
| -rw-r--r-- | sci-biology/raxml/files/raxml-7.2.6-makefile.patch | 29 | ||||
| -rw-r--r-- | sci-biology/raxml/files/raxml-8.2.13-makefile.patch | 37 | ||||
| -rw-r--r-- | sci-biology/raxml/metadata.xml | 11 | ||||
| -rw-r--r-- | sci-biology/raxml/raxml-8.2.13.ebuild (renamed from sci-biology/raxml/raxml-7.2.6.ebuild) | 21 |
5 files changed, 59 insertions, 47 deletions
diff --git a/sci-biology/raxml/Manifest b/sci-biology/raxml/Manifest index 820b570e7e04..cc69c7639d9b 100644 --- a/sci-biology/raxml/Manifest +++ b/sci-biology/raxml/Manifest @@ -1,4 +1,4 @@ -AUX raxml-7.2.6-makefile.patch 786 BLAKE2B d6fc28b20fc3b00b33cefd93fa90f0db255eec642a3fd760baa5489ab90dbb31d9896fe7a595e9f2e4e47b53ab24e1ef2a80486dbe77062f835fce17687a50ae SHA512 955c1403dbae7d5308f10808c3689d04cd4bc6166647fd5d7c6a5eafca45b42f409a22642a57dc19a8f3ce4e00e2e554988ed5a02954ee85ab805759e60beeea -DIST RAxML-7.2.6.tar.bz2 202803 BLAKE2B 579676ff9fad1563eabb9507015acff010977a89ae087df9b828b80bc9352ed44c98faeaf4c8d884ffa14176bfa28772dc9872ad8b5d401aff8b834c728e5f65 SHA512 b0027a7e583e6471a774d9e784a0be1ff63b3824a8cfbebca68bf9e414adab297206ea2d43c9b97456e6acc0a6a15f55ca33983381dd6150f9e7ea71ddecdcd3 -EBUILD raxml-7.2.6.ebuild 902 BLAKE2B 23d2b1a93bf50587d5bcacbaf261ad98eecd4e6d6d86bce62bad4459286bdb678c60ad5699cd22c5d6e03df4fb49ccd95c40bbb30f6ec7990e8f81518709aa66 SHA512 5583a0fcb21f80f1cc1d7fe282f56235b6b0add1699330652f8c6c669cbbb1975eb8e088f566252b897a94e5bb80f2738de538d570951bd7508b5a607324c34f -MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de +AUX raxml-8.2.13-makefile.patch 1996 BLAKE2B 4c11992d1d8575ed54f5b374d7344a7de21dbec2eabb78a74ad894662c3008e2692724a3f7ac9659928bdb0e75a3fd4b6ad3d8c729ebb0ad0dd91c52cfe65d81 SHA512 044adeb9d66f1b8ba628c39914442c57b933957bca73ff856d00963878e8f1055baaf51e4feffb78e3090c7b445f819be3418440fd793340b6e8f65eb80b0e18 +DIST raxml-8.2.13.tar.gz 10201721 BLAKE2B ee48dc599947619d12a54cafef1eee554abc0df30a31ba2fdb501b228dadec9f137acff8f472047f4686304f74d27893696c95ff808baa128c2c3d83539366a1 SHA512 c99dc3f8c8798cda38c644501f474c0261e72c1f3b64d594d5006fa03e8d8c4da3bdf20b8e3c6c9f669c9509d5af27a0c286a2570a54c8ff7df7cd63c1f78885 +EBUILD raxml-8.2.13.ebuild 921 BLAKE2B 2facbdad60a72dc69341aafb8389e28196ba4ef7a9e3bbd71bcb7d0c3f3daedf7bd844798a4456a05344ad80a900936e73a914cee4cfa40d08a47a559aac8036 SHA512 6f2a3e357187c8ec081cd2be94c487263f062cc502e39a77e3c15fad1dad1b3a97ecfa84c2660d2a4a43a12a06bd8547a4710b0ce187dcf11dfab0269cf62e44 +MISC metadata.xml 350 BLAKE2B 7cf3cb5ea8626cadeb2a4709f466742bb1d909c58717aa0988bb4157203db26a7e571d1aec74e1bb73703bcba3f00c6d828d32ea342709a4244f4235bf2313c0 SHA512 6738c142066459babe699d53089935c7c2c1864951cf6a3148beb9015a67ce0dc60e70caa169348126b5b44f7f693b95810b871debacccd91a2643e03820f2ea diff --git a/sci-biology/raxml/files/raxml-7.2.6-makefile.patch b/sci-biology/raxml/files/raxml-7.2.6-makefile.patch deleted file mode 100644 index 6b82ed65b770..000000000000 --- a/sci-biology/raxml/files/raxml-7.2.6-makefile.patch +++ /dev/null @@ -1,29 +0,0 @@ - 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 -+CPPFLAGS += -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) $(LIBS) - - classify.o : classify.c $(GLOBAL_DEPS) - evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS) 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 <peter@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 : + $(RM) *.o raxmlHPC + diff --git a/sci-biology/raxml/metadata.xml b/sci-biology/raxml/metadata.xml index ccdff086e20b..dd68d972db31 100644 --- a/sci-biology/raxml/metadata.xml +++ b/sci-biology/raxml/metadata.xml @@ -1,8 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="github">stamatak/standard-RAxML</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/raxml/raxml-7.2.6.ebuild b/sci-biology/raxml/raxml-8.2.13.ebuild index adb044426381..859016195389 100644 --- a/sci-biology/raxml/raxml-7.2.6.ebuild +++ b/sci-biology/raxml/raxml-8.2.13.ebuild @@ -1,29 +1,30 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit flag-o-matic toolchain-funcs DESCRIPTION="Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees" -HOMEPAGE="http://wwwkramer.in.tum.de/exelixis/software.html" -SRC_URI="http://wwwkramer.in.tum.de/exelixis/software/RAxML-${PV}.tar.bz2" -S="${WORKDIR}/RAxML-${PV}" +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-${PV}" LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="cpu_flags_x86_sse3 +threads" -REQUIRED_USE="cpu_flags_x86_sse3" # mpi is not supported in version 7.2.2. mpi is enabled by adding -DPARALLEL to CFLAGS PATCHES=( "${FILESDIR}"/${P}-makefile.patch ) src_configure() { - use cpu_flags_x86_sse3 && append-cppflags -D__SIM_SSE3 - use threads && \ - append-cppflags -D_USE_PTHREADS && \ - append-libs -pthread + 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 } |