[gentoo-commits] proj/sci:master commit in: sci-biology/mavid/

[gentoo-commits] proj/sci:master commit in: sci-biology/mavid/

[Justin Lecher]

commit:     3e3bd5f1361f0c4c02446b4fac67b9869d1ef8ad
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Nov 10 14:39:09 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Nov 10 14:39:09 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3e3bd5f1

sci-biology/mavid: Bump EAPI

Package-Manager: portage-2.2.14

---
 sci-biology/mavid/ChangeLog          |  6 +++++-
 sci-biology/mavid/mavid-2.0.4.ebuild | 31 +++++++++++++++++++++++--------
 sci-biology/mavid/metadata.xml       | 10 +++++-----
 3 files changed, 33 insertions(+), 14 deletions(-)

diff --git a/sci-biology/mavid/ChangeLog b/sci-biology/mavid/ChangeLog
index 713a8e2..320e337 100644
--- a/sci-biology/mavid/ChangeLog
+++ b/sci-biology/mavid/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-biology/mavid
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  10 Nov 2014; Justin Lecher <jlec@gentoo.org> mavid-2.0.4.ebuild,
+  metadata.xml:
+  Bump EAPI
+
   08 Jul 2008; weaver <weaver@gentoo.org> +metadata.xml,
   +mavid-2.0.4.ebuild:
   New ebuild, bug 207250

diff --git a/sci-biology/mavid/mavid-2.0.4.ebuild b/sci-biology/mavid/mavid-2.0.4.ebuild
index 40d2737..79bead6 100644
--- a/sci-biology/mavid/mavid-2.0.4.ebuild
+++ b/sci-biology/mavid/mavid-2.0.4.ebuild
@@ -2,6 +2,10 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
+EAPI=5
+
+inherit toolchain-funcs
+
 DESCRIPTION="Multiple alignment of large DNA sequences"
 HOMEPAGE="http://baboon.math.berkeley.edu/mavid/"
 SRC_URI="http://bio.math.berkeley.edu/mavid/download/mavid-package-${PV}.tar.gz"
@@ -9,22 +13,33 @@ SRC_URI="http://bio.math.berkeley.edu/mavid/download/mavid-package-${PV}.tar.gz"
 LICENSE="mavid"
 SLOT="0"
 IUSE=""
-KEYWORDS="~x86"
+KEYWORDS="~amd64 ~x86"
 
 DEPEND=""
-RDEPEND="sci-biology/clustalw
+RDEPEND="
+	sci-biology/clustalw
 	sci-biology/fastdnaml"
 
-S="${WORKDIR}/mavid-package-${PV}"
+S="${WORKDIR}"/${PN}-package-${PV}
+
+src_prepare() {
+	sed \
+		-e 's:OPT_CPP_OPTIONS =:OPT_CPP_OPTIONS ?=:g' \
+		-e 's:DEBUG_CPP_OPTIONS =:DEBUG_CPP_OPTIONS ?=:g' \
+		-i $(find -type f -name Makefile) || die
+}
+
+src_compile() {
+	emake \
+		CPP=$(tc-getCXX) \
+		BASE_CPP_OPTIONS="${CXXFLAGS}" \
+		DEBUG_CPP_OPTIONS="${CXXFLAGS}" \
+		OPT_CPP_OPTIONS="${CXXFLAGS}"
 
-src_unpack() {
-	unpack ${A}
-	sed -i 's/\(OPT_CPP_OPTIONS =\)/\1 ${CFLAGS} /' "${S}"/{bioc,mavid}/Makefile || die
-	sed -i 's/\(CPP_OPTIONS =\) -O4/\1 ${CFLAGS} -O4/' "${S}"/utils/*/Makefile || die
-	sed -i 's/$.*_DIRECTORY\///' "${S}"/mavid/mavid.pl || die
 }
 
 src_install() {
+	local i
 	dobin mavid/{mavid,mavid.pl}
 	for i in checkfasta cut_alignment extract_seq extract_tree fasta2phylip phylip2fasta project_alignment randtree root_tree tree_dists; do
 		dobin utils/$i/$i

diff --git a/sci-biology/mavid/metadata.xml b/sci-biology/mavid/metadata.xml
index 3302123..fc7c769 100644
--- a/sci-biology/mavid/metadata.xml
+++ b/sci-biology/mavid/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<maintainer>
-		<email>weaver@gentoo.org</email>
-		<name>Andrey Kislyuk</name>
-	</maintainer>
-	<herd>sci-biology</herd>
+  <maintainer>
+    <email>weaver@gentoo.org</email>
+    <name>Andrey Kislyuk</name>
+  </maintainer>
+  <herd>sci-biology</herd>
 </pkgmetadata>