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@gentoo.org>

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
+}