commit: f462f85a318159798956f27b851268e7fd0c2a16 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Apr 3 17:57:05 2016 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Apr 3 17:57:05 2016 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f462f85a
sci-biology/abyss: Latest ebuild from science-overlay * EAPI=6 Package-Manager: portage-2.2.28 sci-biology/abyss/abyss-1.3.6-r1.ebuild | 54 ++++++++++++++++++++++ sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch | 40 ++++++++++++++++ 2 files changed, 94 insertions(+) diff --git a/sci-biology/abyss/abyss-1.3.6-r1.ebuild b/sci-biology/abyss/abyss-1.3.6-r1.ebuild new file mode 100644 index 0000000..a4327b0 --- /dev/null +++ b/sci-biology/abyss/abyss-1.3.6-r1.ebuild @@ -0,0 +1,54 @@ +# 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="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz"; + +LICENSE="abyss" +SLOT="0" +IUSE="+mpi openmp misc-haskell" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-cpp/sparsehash + dev-libs/boost + misc-haskell? ( dev-libs/gmp:0= + virtual/libffi:0= + ) + mpi? ( virtual/mpi ) +" +DEPEND="${RDEPEND} + misc-haskell? ( dev-lang/ghc + dev-haskell/mmap ) +" + +# todo: --enable-maxk=N configure option +# todo: fix automagic mpi toggling + +PATCHES=( + "${FILESDIR}"/${P}-gcc-4.7.patch + "${FILESDIR}"/${P}-ac_prog_ar.patch + "${FILESDIR}"/${P}-samtoafg.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-1.3.6-samtoafg.patch b/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch new file mode 100644 index 0000000..cb7dfb0 --- /dev/null +++ b/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch @@ -0,0 +1,40 @@ +Hello, + +I see Shaun Jackmans' (abyss-)sam2afg script is available within the +Amos source repository. I find this very useful for coercing output from +assemblers which which don't track read location into amos by remapping +reads against the assembly and converting to afg - not ideal but better +than nothing when you don't have the 'real' read locations to work with. + +This fails, however when reads are aligned with 'bwa mem', which can +output multi-part alignments. sam2afg checks for reuse of the same read +id (presumably to prevent the generation of non-unique eid values), +consequently encountering multiple alignments for a read causes it to die. + +The following one-line patch allows sam2afg to skip these secondary +alignments present in 'bwa mem' output, provided bwa mem has been run +with the '-M' argument which sets the SAM 'secondary alignment' flag on +the alignments in question. + +Hopefully this will also be of use to others... + +Best Regards, +James + +-- +Dr. James Abbott +Lead Bioinformatician +Bioinformatics Support Service +Imperial College, London + + +--- abyss-1.3.6/bin/abyss-samtoafg.ori 2015-05-23 23:43:46.797747928 +0200 ++++ abyss-1.3.6/bin/abyss-samtoafg 2015-05-23 23:44:09.227747743 +0200 +@@ -105,6 +105,7 @@ + die unless defined $qqual; + + $tstart--; # convert to zero-based coordinate ++ next if $flag & 0x100; # secondary alignment + $qid .= "/1" if $flag & 0x40; #FREAD1 + $qid .= "/2" if $flag & 0x80; #FREAD2 +
