* [gentoo-commits] repo/gentoo:master commit in: sci-biology/raxml/, sci-biology/raxml/files/
@ 2021-04-05 14:15 David Seifert
0 siblings, 0 replies; 2+ messages in thread
From: David Seifert @ 2021-04-05 14:15 UTC (permalink / raw
To: gentoo-commits
commit: d3bc203ff48c69ad14e9b659c8d9c3c9d6d85bff
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Apr 5 14:14:38 2021 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Apr 5 14:14:38 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d3bc203f
sci-biology/raxml: Port to EAPI 7
Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/raxml/files/raxml-7.2.6-makefile.patch | 4 ++--
sci-biology/raxml/raxml-7.2.6.ebuild | 25 +++++++++-------------
2 files changed, 12 insertions(+), 17 deletions(-)
diff --git a/sci-biology/raxml/files/raxml-7.2.6-makefile.patch b/sci-biology/raxml/files/raxml-7.2.6-makefile.patch
index ae83e2eef4e..6b82ed65b77 100644
--- a/sci-biology/raxml/files/raxml-7.2.6-makefile.patch
+++ b/sci-biology/raxml/files/raxml-7.2.6-makefile.patch
@@ -14,7 +14,7 @@ index 716b6c6..f0c1de2 100644
-CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -msse
-+CFLAGS += -D_GNU_SOURCE
++CPPFLAGS += -D_GNU_SOURCE
@@ -23,7 +23,7 @@ index 716b6c6..f0c1de2 100644
raxmlHPC : $(objs)
- $(CC) -o raxmlHPC $(objs) $(LIBRARIES)
-+ $(CC) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES)
++ $(CC) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES) $(LIBS)
classify.o : classify.c $(GLOBAL_DEPS)
evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
diff --git a/sci-biology/raxml/raxml-7.2.6.ebuild b/sci-biology/raxml/raxml-7.2.6.ebuild
index 50fffc34acc..adb04442638 100644
--- a/sci-biology/raxml/raxml-7.2.6.ebuild
+++ b/sci-biology/raxml/raxml-7.2.6.ebuild
@@ -1,34 +1,29 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
-inherit eutils flag-o-matic toolchain-funcs
+inherit flag-o-matic toolchain-funcs
DESCRIPTION="Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees"
HOMEPAGE="http://wwwkramer.in.tum.de/exelixis/software.html"
SRC_URI="http://wwwkramer.in.tum.de/exelixis/software/RAxML-${PV}.tar.bz2"
+S="${WORKDIR}/RAxML-${PV}"
-SLOT="0"
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
-DEPEND="" # mpi? ( virtual/mpi )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/RAxML-${PV}"
-
-src_prepare() {
- epatch "${FILESDIR}"/${P}-makefile.patch
+PATCHES=( "${FILESDIR}"/${P}-makefile.patch )
- use cpu_flags_x86_sse3 && append-cflags -D__SIM_SSE3
+src_configure() {
+ use cpu_flags_x86_sse3 && append-cppflags -D__SIM_SSE3
use threads && \
- append-cflags -D_USE_PTHREADS && \
- append-ldflags -pthread
+ append-cppflags -D_USE_PTHREADS && \
+ append-libs -pthread
tc-export CC
}
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/raxml/, sci-biology/raxml/files/
@ 2024-05-24 8:45 David Seifert
0 siblings, 0 replies; 2+ messages in thread
From: David Seifert @ 2024-05-24 8:45 UTC (permalink / raw
To: gentoo-commits
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 <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 :
+ $(RM) *.o raxmlHPC
+
diff --git a/sci-biology/raxml/metadata.xml b/sci-biology/raxml/metadata.xml
index ccdff086e20b..dd68d972db31 100644
--- a/sci-biology/raxml/metadata.xml
+++ b/sci-biology/raxml/metadata.xml
@@ -1,8 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">stamatak/standard-RAxML</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/raxml/raxml-8.2.13.ebuild b/sci-biology/raxml/raxml-8.2.13.ebuild
new file mode 100644
index 000000000000..859016195389
--- /dev/null
+++ b/sci-biology/raxml/raxml-8.2.13.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit flag-o-matic toolchain-funcs
+
+DESCRIPTION="Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees"
+HOMEPAGE="https://github.com/stamatak/standard-RAxML"
+SRC_URI="https://github.com/stamatak/standard-RAxML/archive/refs/tags/v${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
+}
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