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commit: f462f85a318159798956f27b851268e7fd0c2a16 |
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Author: David Seifert <soap <AT> gentoo <DOT> org> |
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AuthorDate: Sun Apr 3 17:57:05 2016 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Sun Apr 3 17:57:05 2016 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f462f85a |
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|
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sci-biology/abyss: Latest ebuild from science-overlay |
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|
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* EAPI=6 |
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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-1.3.6-r1.ebuild | 54 ++++++++++++++++++++++ |
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sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch | 40 ++++++++++++++++ |
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2 files changed, 94 insertions(+) |
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|
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diff --git a/sci-biology/abyss/abyss-1.3.6-r1.ebuild b/sci-biology/abyss/abyss-1.3.6-r1.ebuild |
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new file mode 100644 |
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index 0000000..a4327b0 |
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--- /dev/null |
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+++ b/sci-biology/abyss/abyss-1.3.6-r1.ebuild |
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@@ -0,0 +1,54 @@ |
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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="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz" |
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+ |
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+LICENSE="abyss" |
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+SLOT="0" |
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+IUSE="+mpi openmp misc-haskell" |
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+KEYWORDS="~amd64 ~x86" |
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+ |
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+RDEPEND=" |
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+ dev-cpp/sparsehash |
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+ dev-libs/boost |
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+ misc-haskell? ( dev-libs/gmp:0= |
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+ virtual/libffi:0= |
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+ ) |
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+ mpi? ( virtual/mpi ) |
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+" |
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+DEPEND="${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}-gcc-4.7.patch |
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+ "${FILESDIR}"/${P}-ac_prog_ar.patch |
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+ "${FILESDIR}"/${P}-samtoafg.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-1.3.6-samtoafg.patch b/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch |
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new file mode 100644 |
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index 0000000..cb7dfb0 |
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--- /dev/null |
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+++ b/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch |
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@@ -0,0 +1,40 @@ |
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+Hello, |
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+ |
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+I see Shaun Jackmans' (abyss-)sam2afg script is available within the |
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+Amos source repository. I find this very useful for coercing output from |
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+assemblers which which don't track read location into amos by remapping |
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+reads against the assembly and converting to afg - not ideal but better |
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+than nothing when you don't have the 'real' read locations to work with. |
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+ |
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+This fails, however when reads are aligned with 'bwa mem', which can |
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+output multi-part alignments. sam2afg checks for reuse of the same read |
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+id (presumably to prevent the generation of non-unique eid values), |
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+consequently encountering multiple alignments for a read causes it to die. |
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+ |
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+The following one-line patch allows sam2afg to skip these secondary |
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+alignments present in 'bwa mem' output, provided bwa mem has been run |
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+with the '-M' argument which sets the SAM 'secondary alignment' flag on |
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+the alignments in question. |
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+ |
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+Hopefully this will also be of use to others... |
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+ |
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+Best Regards, |
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+James |
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+ |
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+-- |
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+Dr. James Abbott |
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+Lead Bioinformatician |
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+Bioinformatics Support Service |
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+Imperial College, London |
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+ |
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+ |
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+--- abyss-1.3.6/bin/abyss-samtoafg.ori 2015-05-23 23:43:46.797747928 +0200 |
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++++ abyss-1.3.6/bin/abyss-samtoafg 2015-05-23 23:44:09.227747743 +0200 |
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+@@ -105,6 +105,7 @@ |
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+ die unless defined $qqual; |
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+ |
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+ $tstart--; # convert to zero-based coordinate |
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++ next if $flag & 0x100; # secondary alignment |
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+ $qid .= "/1" if $flag & 0x40; #FREAD1 |
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+ $qid .= "/2" if $flag & 0x80; #FREAD2 |
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+ |