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/clustalw-mpi/Manifest                  |  6 ++++
 .../clustalw-mpi/clustalw-mpi-0.13-r2.ebuild       | 39 ++++++++++++++++++++++
 sci-biology/clustalw-mpi/files/0.13-gentoo.patch   | 23 +++++++++++++
 sci-biology/clustalw-mpi/metadata.xml              | 14 ++++++++
 4 files changed, 82 insertions(+)
 create mode 100644 sci-biology/clustalw-mpi/Manifest
 create mode 100644 sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild
 create mode 100644 sci-biology/clustalw-mpi/files/0.13-gentoo.patch
 create mode 100644 sci-biology/clustalw-mpi/metadata.xml

(limited to 'sci-biology/clustalw-mpi')

diff --git a/sci-biology/clustalw-mpi/Manifest b/sci-biology/clustalw-mpi/Manifest
new file mode 100644
index 000000000000..62795800b403
--- /dev/null
+++ b/sci-biology/clustalw-mpi/Manifest
@@ -0,0 +1,6 @@
+AUX 0.13-gentoo.patch 596 SHA256 10eb9b964fd565833542075a470f70cb4b5624f436b661f442d6951bcf6ebc4a SHA512 4b0350f9ca8ce0d6e098faae5749bdc120b853dec745a07899e81bb195623affe46560d28a3c79db7af57551c9c873d91e693ee30a5c185ac4d2adb26a9d27c8 WHIRLPOOL ec786caa4e73a6a51c643bd756f3f8f6b1dc837c05d57b3fddaddffb52c1b378d00ab48af96992a5c4093874effaa90133e14a1d6e87f7e970a309e246341aa3
+DIST clustalw-mpi-0.13.tar.gz 154911 SHA256 2fcb0dc0001b034f2931153654fc66d67db360f0bf3fbcde19dc389bbe145845 SHA512 e0008accb6c07584dc5ad1b953e0c668fad43ca3a86d88dbcf50fbfa858870131e4db005cc87b46f5268cd0795e9a2ce01326d8318d66b694a92b85e6f9635df WHIRLPOOL 850e1f8daff5aeede4bc47779bafa7f331017b854c2f0926fb31b6c40aaf79fb5f8e7605bddee5a9d52043313b578bf1f4e14f060c387ee1ec6e65170fd9fcd7
+EBUILD clustalw-mpi-0.13-r2.ebuild 962 SHA256 4a27734b4e9d3b5b435b7116198acc2038d604be791f1d926770cef8455c8b1b SHA512 48cd3c0ff42cf9c5185e70d0fbdb1b21020a7ad75156adba06346b7cd6847dfbb2752164edd93238890ef55d38565cdcc196355094ca3e8e253f3d508b409ef3 WHIRLPOOL 735ada0efe55c89871fa4ab658d8179632f232d8ca8b1e8f593423e103295cfa6b5d7a965f42901aab50feeab18a6ef619aa9bd38ab6e027b0651e61546b2d7f
+MISC ChangeLog 2868 SHA256 a40d8ca1cc9be26f63bd2d65ec0af55cf15fca402851958bc0101816e235bd33 SHA512 cc8e4dbae133e4b4a076afeeb64cc20fdbe7e17bab16f51861394c7e033c0e5444f53350089d6fb7f387a31f2b057631bf8b58f7c1d2b075303bfc78e1e39b83 WHIRLPOOL 3b6d67855b3d5f3df6dc011910d30dfb61d2ebac562766897495df91fef3c10665bf7917a09f8679d1b5db794eb1a2a52e27435ca46c8dbff748d88ee57653f0
+MISC ChangeLog-2015 1225 SHA256 f8b8e736c5c507e369ac2086f005afd8d8c370787e3660e273a60418ac13991e SHA512 1e75b3049bd51f5c38eb442cb102a9d177c24ed48a681b66c5993f2605c42d24b3243cb0c0c01a0552e276c75085d8ae48acf5d32c6f420e3067f89030ca9e64 WHIRLPOOL 27a9a93ec382ed58ceaf428a84fc7a537913532ae55684d9486e9f635895c8053b85c10da1fc9dbb10524a2bb59efbb37e77673b78b871a2ac0c12cca3a8605f
+MISC metadata.xml 491 SHA256 0e59732460a71918988171079534c51664ead8f709d1d88b7078a19741cdd707 SHA512 d242bee2ea381f992deb30b406b89ec2da08e1d513da5d9a94016ea07247670744d25bac8175607291c39d80090d3d1746154d3c60ba95bdd720d57c0212b3d0 WHIRLPOOL ef93fe44fc1a7c7efa0c2464a5dac277714f5b16e75b1803709441493475724227bee8d6fd214d2f60ab6c6f444f4d1c4466975b44c864df0c63a42e5abdd7d3
diff --git a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild
new file mode 100644
index 000000000000..76d3b80cde32
--- /dev/null
+++ b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs
+
+DESCRIPTION="An MPI implemention of the ClustalW general purpose multiple alignment algorithm"
+HOMEPAGE="http://www.bii.a-star.edu.sg/achievements/applications/clustalw/index.php"
+SRC_URI="http://web.bii.a-star.edu.sg/~kuobin/${PN}/${P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="mpi_njtree static_pairalign"
+
+DEPEND="virtual/mpi"
+RDEPEND="${DEPEND}"
+
+PATCHES=( "${FILESDIR}"/${PV}-gentoo.patch )
+
+src_prepare() {
+	default
+
+	if use mpi_njtree; then
+		sed -e "s/TREES_FLAG/#TREES_FLAG/" -i Makefile || \
+			die "Failed to configure MPI code for NJ trees"
+	fi
+
+	if use static_pairalign; then
+		sed -e "s/DDYNAMIC_SCHEDULING/DSTATIC_SCHEDULING/" -i Makefile || \
+			die "Failed to configure static scheduling for pair alignments"
+	fi
+}
+
+src_install() {
+	dobin ${PN}
+	newdoc README.${PN} README
+}
diff --git a/sci-biology/clustalw-mpi/files/0.13-gentoo.patch b/sci-biology/clustalw-mpi/files/0.13-gentoo.patch
new file mode 100644
index 000000000000..6e36061cbb39
--- /dev/null
+++ b/sci-biology/clustalw-mpi/files/0.13-gentoo.patch
@@ -0,0 +1,23 @@
+ Makefile |    6 +++---
+ 1 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index f2107ce..835232b 100644
+--- a/Makefile
++++ b/Makefile
+@@ -25,12 +25,12 @@ TREES_FLAG = -DSERIAL_NJTREE
+ PAIRALIGN_FLAG = -DDYNAMIC_SCHEDULING_PAIRALIGN 
+ #PAIRALIGN_FLAG = -DSTATIC_SCHEDULING_PAIRALIGN
+ 
+-CFLAGS  = -c -O3
++CFLAGS  += -c
+ #CFLAGS  = -c -O3 -funroll-all-loops
+-LFLAGS	= -lm 
++LIBS	= -lm 
+ 
+ clustalw-mpi: $(OBJECTS) 
+-	$(CC) -o $@ $(OBJECTS) $(LFLAGS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJECTS) $(LIBS)
+ 
+ interface.o : interface.c $(HEADERS) param.h
+ 	$(CC) $(CFLAGS) $*.c
diff --git a/sci-biology/clustalw-mpi/metadata.xml b/sci-biology/clustalw-mpi/metadata.xml
new file mode 100644
index 000000000000..8ab4494152c8
--- /dev/null
+++ b/sci-biology/clustalw-mpi/metadata.xml
@@ -0,0 +1,14 @@
+<?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>
+<use>
+  <flag name="mpi_njtree">Use MPI (as opposed to serial) code for computing
+    neighbor-joining trees</flag>
+  <flag name="static_pairalign">Use static (as opposed to dynamic) scheduling
+    for pair alignments</flag>
+</use>
+</pkgmetadata>
-- 
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