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 +}
