[gentoo-commits] repo/gentoo:master commit in: sci-biology/maq/, sci-biology/maq/files/

[David Seifert]

commit:     1be892e848feb9c23c9b1b99dbf6883d51075636
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Feb  6 20:48:02 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Feb  6 21:26:35 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1be892e8

sci-biology/maq: Modernise to EAPI 6

Package-Manager: Portage-2.3.3, Repoman-2.3.1
Closes: https://github.com/gentoo/gentoo/pull/3856

 .../maq/files/maq-0.7.1-remove-64bit-flag.patch    | 19 ++++++++++
 sci-biology/maq/maq-0.7.1-r2.ebuild                | 43 ++++++++++++++++++++++
 2 files changed, 62 insertions(+)

diff --git a/sci-biology/maq/files/maq-0.7.1-remove-64bit-flag.patch b/sci-biology/maq/files/maq-0.7.1-remove-64bit-flag.patch
new file mode 100644
index 00000000..3bcbc2b
--- /dev/null
+++ b/sci-biology/maq/files/maq-0.7.1-remove-64bit-flag.patch
@@ -0,0 +1,19 @@
+Do not hardcode -m64 into the build system
+
+--- a/configure.ac
++++ b/configure.ac
+@@ -21,12 +21,12 @@
+ 						   [ext_CFLAGS="-arch x86_64 -arch i386 -arch ppc64 -arch ppc"],
+ 						   [ext_CFLAGS="-arch i386 -arch ppc"]);;
+ 	  0) CFLAGS="-m64"
+-	  	 AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS="-m64"], []);;
++	  	 AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS=""], []);;
+ 	esac;;
+   *)
+     AC_MSG_CHECKING([if gcc accepts -m64])
+     CFLAGS="-m64"
+-    AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS="-m64"; AC_MSG_RESULT([yes])],
++    AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS=""; AC_MSG_RESULT([yes])],
+ 					  [ext_CFLAGS="-D_FILE_OFFSET_BITS=64"; AC_MSG_RESULT([no])]);;
+ esac
+ AC_ARG_ENABLE(experimental, [  --enable-experimental   enable experimental features],

diff --git a/sci-biology/maq/maq-0.7.1-r2.ebuild b/sci-biology/maq/maq-0.7.1-r2.ebuild
new file mode 100644
index 00000000..fb01400
--- /dev/null
+++ b/sci-biology/maq/maq-0.7.1-r2.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit autotools
+
+DESCRIPTION="Mapping and Assembly with Qualities, mapping NGS reads to reference genomes"
+HOMEPAGE="http://maq.sourceforge.net/"
+SRC_URI="
+	mirror://sourceforge/${PN}/${P}.tar.bz2
+	mirror://sourceforge/${PN}/calib-36.dat.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND="sys-libs/zlib"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-flags.patch
+	"${FILESDIR}"/${P}-bfr-overfl.patch
+	"${FILESDIR}"/${P}-gcc-4.7.patch
+	"${FILESDIR}"/${P}-remove-64bit-flag.patch
+)
+
+src_prepare() {
+	default
+	eautoreconf
+}
+
+src_install() {
+	default
+
+	insinto /usr/share/${PN}
+	doins "${WORKDIR}"/*.dat
+
+	doman maq.1
+	dodoc ${PN}.pdf
+}