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commit: e09e5ec884dd0210694529c19b81fab9c48a76bc |
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Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Tue Sep 11 21:54:18 2018 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Tue Sep 11 21:54:18 2018 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e09e5ec8 |
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|
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sci-biology/abyss: version bump |
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|
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An improved version with sealer using OpenMP+OpenMPI now. |
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|
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https://github.com/bcgsc/abyss/releases/tag/2.1.1 |
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|
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Package-Manager: Portage-2.3.48, Repoman-2.3.10 |
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|
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sci-biology/abyss/abyss-2.1.1.ebuild | 54 ++++++++++++++++++++++++++++++++++++ |
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sci-biology/abyss/metadata.xml | 18 ++++++++++++ |
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2 files changed, 72 insertions(+) |
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|
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diff --git a/sci-biology/abyss/abyss-2.1.1.ebuild b/sci-biology/abyss/abyss-2.1.1.ebuild |
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new file mode 100644 |
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index 000000000..ccce937c7 |
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--- /dev/null |
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+++ b/sci-biology/abyss/abyss-2.1.1.ebuild |
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@@ -0,0 +1,54 @@ |
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+# Copyright 1999-2018 Gentoo Foundation |
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+# Distributed under the terms of the GNU General Public License v2 |
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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/${PV}.tar.gz -> ${P}.tar.gz" |
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+ |
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+LICENSE="abyss" |
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+SLOT="0" |
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+IUSE="+mpi openmp misc-haskell" |
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+KEYWORDS="~amd64 ~x86" |
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+ |
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+RDEPEND=" |
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+ dev-cpp/sparsehash |
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+ dev-libs/boost:= |
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+ misc-haskell? ( |
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+ dev-libs/gmp:0= |
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+ virtual/libffi:0= |
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+ ) |
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+ mpi? ( sys-cluster/openmpi )" |
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+DEPEND="${RDEPEND} |
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+ misc-haskell? ( |
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+ dev-lang/ghc |
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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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+pkg_pretend() { |
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+ [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp |
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+} |
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+ |
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+pkg_setup() { |
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+ [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp |
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+} |
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+ |
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+src_prepare() { |
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+ default |
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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/metadata.xml b/sci-biology/abyss/metadata.xml |
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new file mode 100644 |
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index 000000000..47116e507 |
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--- /dev/null |
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+++ b/sci-biology/abyss/metadata.xml |
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@@ -0,0 +1,18 @@ |
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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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+ <upstream> |
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+ <remote-id type="github">bcgsc/abyss</remote-id> |
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+ </upstream> |
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+</pkgmetadata> |