commit: 76c8aa5fabb5f1ae43d4fdf831bcf94b7e6e09a6 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Thu Jun 30 22:02:59 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Thu Jun 30 22:02:59 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=76c8aa5f
sci-biology/abyss: version bump, update SRC_URI Package-Manager: portage-2.2.28 sci-biology/abyss/abyss-1.9.0.ebuild | 52 ++++++++++++++++++++++ .../abyss/files/abyss-1.9.0-ac_prog_ar.patch | 18 ++++++++ sci-biology/abyss/metadata.xml | 15 +++++++ 3 files changed, 85 insertions(+) diff --git a/sci-biology/abyss/abyss-1.9.0.ebuild b/sci-biology/abyss/abyss-1.9.0.ebuild new file mode 100644 index 0000000..b2de141 --- /dev/null +++ b/sci-biology/abyss/abyss-1.9.0.ebuild @@ -0,0 +1,52 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +inherit autotools toolchain-funcs + +DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" +HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"; +SRC_URI="https://github.com/bcgsc/abyss/archive/1.9.0.tar.gz -> ${P}.tar.gz" + +LICENSE="abyss" +SLOT="0" +IUSE="+mpi openmp misc-haskell" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-cpp/sparsehash + dev-libs/boost + misc-haskell? ( dev-libs/gmp:0= + virtual/libffi:0= + ) + mpi? ( virtual/mpi ) +" +DEPEND="${RDEPEND} + misc-haskell? ( dev-lang/ghc + dev-haskell/mmap ) +" + +# todo: --enable-maxk=N configure option +# todo: fix automagic mpi toggling + +PATCHES=( + "${FILESDIR}"/${P}-ac_prog_ar.patch +) + +src_prepare() { + default + tc-export AR + sed -i -e "s/-Werror//" configure.ac || die #365195 + sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die + eautoreconf +} + +src_configure() { + # disable building haskell tool Misc/samtobreak + # unless request by user: bug #534412 + use misc-haskell || export ac_cv_prog_ac_ct_GHC= + + econf $(use_enable openmp) +} diff --git a/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch new file mode 100644 index 0000000..158e9b1 --- /dev/null +++ b/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch @@ -0,0 +1,18 @@ + configure.ac | 4 ++++ + 1 file changed, 4 insertions(+) + +diff --git a/configure.ac b/configure.ac +index 9d4bb66..aa94364 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -12,6 +12,10 @@ AC_PROG_CPP + AC_PROG_CXX + AC_PROG_INSTALL + AC_PROG_RANLIB ++AN_MAKEVAR([AR], [AC_PROG_AR]) ++AN_PROGRAM([ar], [AC_PROG_AR]) ++AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)]) ++AC_PROG_AR + AC_CHECK_TOOL(GHC, ghc) + AM_CONDITIONAL([HAVE_GHC], [test "$GHC"]) + diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml new file mode 100644 index 0000000..c0c84f0 --- /dev/null +++ b/sci-biology/abyss/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biol...@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <maintainer type="project"> + <email>hask...@gentoo.org</email> + <name>Gentoo Haskell</name> + </maintainer> + <use> + <flag name='misc-haskell'>build abyss-samtobreak tool, pull in haskell toolchain</flag> + </use> +</pkgmetadata>
