From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001
From: V3n3RiX <venerix@redcorelinux.org>
Date: Mon, 9 Oct 2017 18:53:29 +0100
Subject: reinit the tree, so we can have metadata

---
 sci-biology/muscle/Manifest                |  6 ++++++
 sci-biology/muscle/files/3.8.31-make.patch | 26 ++++++++++++++++++++++++
 sci-biology/muscle/metadata.xml            |  8 ++++++++
 sci-biology/muscle/muscle-3.8.31.ebuild    | 32 ++++++++++++++++++++++++++++++
 4 files changed, 72 insertions(+)
 create mode 100644 sci-biology/muscle/Manifest
 create mode 100644 sci-biology/muscle/files/3.8.31-make.patch
 create mode 100644 sci-biology/muscle/metadata.xml
 create mode 100644 sci-biology/muscle/muscle-3.8.31.ebuild

(limited to 'sci-biology/muscle')

diff --git a/sci-biology/muscle/Manifest b/sci-biology/muscle/Manifest
new file mode 100644
index 000000000000..bde9de2c7a11
--- /dev/null
+++ b/sci-biology/muscle/Manifest
@@ -0,0 +1,6 @@
+AUX 3.8.31-make.patch 989 SHA256 f5352a5fc8a792d7af177d1e829a33e59bc39dedb81baf17c6424f8520ea6879 SHA512 e528b032d4e60d2ca22de1129da56125b8915ed288ee25965b2bc5b1d6118d1d589fa632dac9829011a405c3189b8b6b6c056eedde9dd30a9b6a6f572a5e2d2c WHIRLPOOL db552ae2482532c6034c86eb9be71eb99652e1d24e2031545eb5eff7ab558775ae0bcd0f467520df0a6b47ced18d8f163b7fbe83a1b6642118c86a53e8c7a298
+DIST muscle3.8.31_src.tar.gz 515267 SHA256 43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad SHA512 2baf2aae354ae1e3f529e627be2ace86e89dd15567e1f642a625b63f08ebe3d4bd7315080c7d786d95e3eda8703545ec74af9fe83ad1523d55d00137fb7274ce WHIRLPOOL daea88aaeaaacf5a2da68484010091ae46c69713659f92f45e5e2096af9e7d8c645d14e5b6c4c8e73e4df35a086dee823fcab6d442cd3881b773fb0113ce897d
+EBUILD muscle-3.8.31.ebuild 602 SHA256 3c6964a7120eaf9475c1f0fef930d1c6600f9bf11c008d2b48522b86a749a387 SHA512 4167a3402188bc2b17baa5419fae65e1a10c5884d8419de929434e3d44d985889a5131d34dae3854bc58e25450ccbc055d38839255a8153eb2e4d19ae3b84253 WHIRLPOOL cdc987d2a25f1a8ce40dcd1a83768d0be93f07a1714e4f0b838d93421e87b8365d1fdfdaab8f3140f7d6205e386db884ccb29897896fd4100d2d74b290b5bf01
+MISC ChangeLog 2490 SHA256 1475383b3dd7942a2228d52084ac201a41f8babd48ce1dc6da66e1bc9aafb850 SHA512 d0b774921811864d0e769c67df5464f126ea0c1d179993d7cdf35ec2f69e8dfe4e9e7d2567e6d0389ec740da1ae504107c0677f8d90791166c06cab06e341b1a WHIRLPOOL 49655b6305d974699ab9d268f649b52d209b7c8543c3877ded60f09771fb77d1037b17be062b875de91065294f80d61c98d6977d88bab8fc30040e7e496ebf65
+MISC ChangeLog-2015 2692 SHA256 fa708ddf75b2d3d4fb6b3167e43f157d99a5c9354d919baae3777fbeeee3c52f SHA512 76d9a7bb9b1ab7775c645be47dc5bb01a8482535b540d1983d5f8e15012514746892a67422ae56241e8ea40b521a28759c95c056df5c4b3a870af2e3d51cade9 WHIRLPOOL 86868989b062eac44e05a750955c207ca3577557b138934ab6842e98f34c4af84f9b97a569fe18b0a5cf61c8ebb62f8c10b5d3f4da5afe5a1fa9b836b2c9a0f5
+MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13
diff --git a/sci-biology/muscle/files/3.8.31-make.patch b/sci-biology/muscle/files/3.8.31-make.patch
new file mode 100644
index 000000000000..7c0e7308df54
--- /dev/null
+++ b/sci-biology/muscle/files/3.8.31-make.patch
@@ -0,0 +1,26 @@
+diff --git a/src/mk b/src/mk
+index 475d25a..d4b7e83 100755
+--- a/src/mk
++++ b/src/mk
+@@ -5,17 +5,14 @@ ObjNames='aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln
+ rm -f *.o muscle.make.stdout.txt muscle.make.stderr.txt
+ for CPPName in $CPPNames
+ do
+-  echo $CPPName >> /dev/tty
+-  g++ $ENV_GCC_OPTS -c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $CPPName.cpp -o $CPPName.o  >> muscle.make.stdout.txt 2>> muscle.make.stderr.txt
++  echo "${CXX} ${CXXFLAGS} -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $CPPName.cpp -o $CPPName.o"
++  ${CXX} ${CXXFLAGS} -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $CPPName.cpp -o $CPPName.o
+ done
+ 
+ LINK_OPTS=
+ if [ `uname -s` == Linux ] ; then
+     LINK_OPTS=-static
+ fi
+-g++ $LINK_OPTS $ENV_LINK_OPTS -g -o muscle $ObjNames  >> muscle.make.stdout.txt 2>> muscle.make.stderr.txt
+-tail muscle.make.stderr.txt
+ 
+-strip muscle
+-ls -lh muscle
+-sum muscle
++echo "${CXX} ${LDFLAGS} -o muscle $ObjNames"
++${CXX} ${LDFLAGS} -o muscle $ObjNames
diff --git a/sci-biology/muscle/metadata.xml b/sci-biology/muscle/metadata.xml
new file mode 100644
index 000000000000..959160fe46b1
--- /dev/null
+++ b/sci-biology/muscle/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/muscle/muscle-3.8.31.ebuild b/sci-biology/muscle/muscle-3.8.31.ebuild
new file mode 100644
index 000000000000..1e62a9d28eee
--- /dev/null
+++ b/sci-biology/muscle/muscle-3.8.31.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+MY_P="${PN}${PV}_src"
+
+DESCRIPTION="Multiple sequence comparison by log-expectation"
+HOMEPAGE="http://www.drive5.com/muscle/"
+SRC_URI="http://www.drive5.com/muscle/downloads${PV}/${MY_P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="amd64 ppc x86"
+IUSE=""
+
+RDEPEND="!sci-libs/libmuscle"
+DEPEND=""
+
+S="${WORKDIR}"/${PN}${PV}/src
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-make.patch
+	tc-export CXX
+}
+
+src_install() {
+	dobin "${PN}"
+	dodoc *.txt
+}
-- 
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