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