sci-biology/exonerate-gff3: an improved version of exonerate-2.2.0 with GFF3 format output support

4 files changed, 89 insertions, 0 deletions

diff --git a/sci-biology/exonerate-gff3/ChangeLog b/sci-biology/exonerate-gff3/ChangeLog
new file mode 100644
index 000000000..fc492c85e
--- /dev/null
+++ b/sci-biology/exonerate-gff3/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-biology/exonerate-gff3
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*exonerate-gff3-2.2.0-r1 (30 Mar 2015)
+
+  30 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +exonerate-gff3-2.2.0-r1.ebuild, +files/exonerate-gff3-2.2.0-asneeded.patch,
+  +metadata.xml:
+  sci-biology/exonerate-gff3: an improved version of exonerate-2.2.0 with GFF3
+  format output support
+
diff --git a/sci-biology/exonerate-gff3/exonerate-gff3-2.2.0-r1.ebuild b/sci-biology/exonerate-gff3/exonerate-gff3-2.2.0-r1.ebuild
new file mode 100644
index 000000000..fd2472821
--- /dev/null
+++ b/sci-biology/exonerate-gff3/exonerate-gff3-2.2.0-r1.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/exonerate/exonerate-2.2.0-r1.ebuild,v 1.5 2013/01/25 16:24:50 jlec Exp $
+
+EAPI=4
+
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils toolchain-funcs git-r3
+
+DESCRIPTION="exonerate-2.2.0 with patches to add GFF3 formatted output"
+HOMEPAGE="https://github.com/hotdogee/exonerate-gff3"
+EGIT_REPO_URI="https://github.com/hotdogee/exonerate-gff3.git"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="utils test threads"
+
+REQUIRED_USE="test? ( utils )"
+
+# block with sci-biology/exonerate , maybe the best would be to change SRC_URI in sci-biology/exonerate
+DEPEND="
+	!sci-biology/exonerate
+	dev-libs/glib:2"
+RDEPEND="${DEPEND}"
+
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+PATCHES=( "${FILESDIR}"/${P}-asneeded.patch )
+
+src_prepare() {
+	tc-export CC
+	sed \
+		-e 's: -O3 -finline-functions::g' \
+		-i configure.in || die
+	autotools-utils_src_prepare
+}
+
+src_configure() {
+	local myeconfargs=(
+		$(use_enable utils utilities)
+		$(use_enable threads pthreads)
+		--enable-largefile
+		--enable-glib2
+	)
+	autotools-utils_src_configure
+}
+
+src_install() {
+	autotools-utils_src_install
+	doman doc/man/man1/*.1
+}
diff --git a/sci-biology/exonerate-gff3/files/exonerate-gff3-2.2.0-asneeded.patch b/sci-biology/exonerate-gff3/files/exonerate-gff3-2.2.0-asneeded.patch
new file mode 100644
index 000000000..3268055cd
--- /dev/null
+++ b/sci-biology/exonerate-gff3/files/exonerate-gff3-2.2.0-asneeded.patch
@@ -0,0 +1,15 @@
+Fix build with --as-needed
+
+https://bugs.gentoo.org/268094
+
+--- configure.in
++++ configure.in
+@@ -289,7 +289,7 @@
+ if test "$enable_pthreads" = yes; then
+     echo "Using PTHREADS"
+     CFLAGS="$CFLAGS -DUSE_PTHREADS"
+-    LDFLAGS="$LDFLAGS -lpthread"
++    LIBS="$LIBS -lpthread"
+ elif test "$enable_pthreads" = no; then
+     echo "Not using pthreads"
+ else
diff --git a/sci-biology/exonerate-gff3/metadata.xml b/sci-biology/exonerate-gff3/metadata.xml
new file mode 100644
index 000000000..2bc893037
--- /dev/null
+++ b/sci-biology/exonerate-gff3/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>