commit: 9c102d9aebd555a1db337e89911a198ba8274b55 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Apr 3 18:04:28 2016 +0000 Commit: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de> CommitDate: Sun Apr 3 18:04:28 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9c102d9a
sci-biology/abyss: moved to main tree sci-biology/abyss/abyss-1.3.3-r1.ebuild | 42 --------------- sci-biology/abyss/abyss-1.3.4-r1.ebuild | 47 ----------------- sci-biology/abyss/abyss-1.3.6-r1.ebuild | 59 ---------------------- .../abyss/files/abyss-1.3.3-ac_prog_ar.patch | 18 ------- sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch | 15 ------ sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch | 40 --------------- sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch | 15 ------ sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch | 40 --------------- .../abyss/files/abyss-1.3.6-ac_prog_ar.patch | 18 ------- sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch | 15 ------ sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch | 40 --------------- sci-biology/abyss/metadata.xml | 15 ------ 12 files changed, 364 deletions(-) diff --git a/sci-biology/abyss/abyss-1.3.3-r1.ebuild b/sci-biology/abyss/abyss-1.3.3-r1.ebuild deleted file mode 100644 index 76f15b4..0000000 --- a/sci-biology/abyss/abyss-1.3.3-r1.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -inherit autotools eutils 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/${P}.tar.gz"; - -LICENSE="abyss" -SLOT="0" -IUSE="+mpi openmp" -KEYWORDS="~amd64 ~x86" - -DEPEND=" - dev-cpp/sparsehash - mpi? ( virtual/mpi )" -RDEPEND="${DEPEND}" - -# todo: --enable-maxk=N configure option -# todo: fix automagic mpi toggling - -src_prepare() { - tc-export AR - epatch \ - "${FILESDIR}"/${P}-gcc-4.7.patch \ - "${FILESDIR}"/${P}-ac_prog_ar.patch \ - "${FILESDIR}"/${P}-samtoafg.patch - - sed -i -e "s/-Werror//" configure.ac || die #365195 - sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die - eautoreconf -} - -src_configure() { - econf \ - --docdir="${EPREFIX}/usr/share/doc/${PF}" \ - $(use_enable openmp) -} diff --git a/sci-biology/abyss/abyss-1.3.4-r1.ebuild b/sci-biology/abyss/abyss-1.3.4-r1.ebuild deleted file mode 100644 index 762d49a..0000000 --- a/sci-biology/abyss/abyss-1.3.4-r1.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -AUTOTOOLS_AUTORECONF=true - -inherit autotools-utils - -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/${P}.tar.gz"; - -LICENSE="abyss" -SLOT="0" -IUSE="+mpi openmp" -KEYWORDS="~amd64 ~x86" - -DEPEND=" - dev-cpp/sparsehash - mpi? ( virtual/mpi )" -RDEPEND="${DEPEND}" - -# todo: --enable-maxk=N configure option -# todo: fix automagic mpi toggling - -PATCHES=( - "${FILESDIR}"/${P}-gcc-4.7.patch - "${FILESDIR}"/${PN}-1.3.3-ac_prog_ar.patch - "${FILESDIR}"/${P}-samtoafg.patch - ) - -src_prepare() { - tc-export AR - sed -i -e "s/-Werror//" configure.ac || die #365195 - sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die - autotools-utils_src_prepare -} - -src_configure() { - local myeconfargs=( - --docdir="${EPREFIX}/usr/share/doc/${PF}" - $(use_enable openmp) - ) - autotools-utils_src_configure -} diff --git a/sci-biology/abyss/abyss-1.3.6-r1.ebuild b/sci-biology/abyss/abyss-1.3.6-r1.ebuild deleted file mode 100644 index a449c72..0000000 --- a/sci-biology/abyss/abyss-1.3.6-r1.ebuild +++ /dev/null @@ -1,59 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -AUTOTOOLS_AUTORECONF=true - -inherit autotools-utils - -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() { - tc-export AR - sed -i -e "s/-Werror//" configure.ac || die #365195 - sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die - autotools-utils_src_prepare -} - -src_configure() { - # disable building haskell tool Misc/samtobreak - # unless request by user: bug #534412 - use misc-haskell || export ac_cv_prog_ac_ct_GHC= - - local myeconfargs=( - --docdir="${EPREFIX}/usr/share/doc/${PF}" - $(use_enable openmp) - ) - autotools-utils_src_configure -} diff --git a/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch deleted file mode 100644 index 300868f..0000000 --- a/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch +++ /dev/null @@ -1,18 +0,0 @@ - configure.ac | 4 ++++ - 1 file changed, 4 insertions(+) - -diff --git a/configure.ac b/configure.ac -index 5c6cb92..b99bedd 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 - - # Checks for header files. - AC_CHECK_HEADERS([dlfcn.h fcntl.h float.h limits.h \ diff --git a/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch deleted file mode 100644 index 42066f7..0000000 --- a/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch +++ /dev/null @@ -1,15 +0,0 @@ - ParseAligns/abyss-fixmate.cc | 1 + - 1 files changed, 1 insertions(+), 0 deletions(-) - -diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc -index 506ea0c..a0a403c 100644 ---- a/ParseAligns/abyss-fixmate.cc -+++ b/ParseAligns/abyss-fixmate.cc -@@ -15,6 +15,7 @@ - #include <iterator> - #include <sstream> - #include <string> -+#include <unistd.h> - - using namespace std; - diff --git a/sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch b/sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch deleted file mode 100644 index cb7dfb0..0000000 --- a/sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch +++ /dev/null @@ -1,40 +0,0 @@ -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 - diff --git a/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch deleted file mode 100644 index c2cc35c..0000000 --- a/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch +++ /dev/null @@ -1,15 +0,0 @@ - ParseAligns/abyss-fixmate.cc | 1 + - 1 files changed, 1 insertions(+), 0 deletions(-) - -diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc -index 1a169cf..36cc05b 100644 ---- a/ParseAligns/abyss-fixmate.cc -+++ b/ParseAligns/abyss-fixmate.cc -@@ -16,6 +16,7 @@ - #include <iterator> - #include <sstream> - #include <string> -+#include <unistd.h> - - using namespace std; - diff --git a/sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch b/sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch deleted file mode 100644 index cb7dfb0..0000000 --- a/sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch +++ /dev/null @@ -1,40 +0,0 @@ -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 $flag & 0x80; #FREAD2 - diff --git a/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch deleted file mode 100644 index 158e9b1..0000000 --- a/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch +++ /dev/null @@ -1,18 +0,0 @@ - configure.ac | 4 ++++ - 1 file changed, 4 insertions(+) - -diff --git a/configure.ac b/configure.ac -index 9d4bb66..aa94364 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -12,6 +12,10 @@ AC_PROG_CPP - AC_PROG_CXX - AC_PROG_INSTALL - AC_PROG_RANLIB -+AN_MAKEVAR([AR], [AC_PROG_AR]) -+AN_PROGRAM([ar], [AC_PROG_AR]) -+AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)]) -+AC_PROG_AR - AC_CHECK_TOOL(GHC, ghc) - AM_CONDITIONAL([HAVE_GHC], [test "$GHC"]) - diff --git a/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch deleted file mode 100644 index c2cc35c..0000000 --- a/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch +++ /dev/null @@ -1,15 +0,0 @@ - ParseAligns/abyss-fixmate.cc | 1 + - 1 files changed, 1 insertions(+), 0 deletions(-) - -diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc -index 1a169cf..36cc05b 100644 ---- a/ParseAligns/abyss-fixmate.cc -+++ b/ParseAligns/abyss-fixmate.cc -@@ -16,6 +16,7 @@ - #include <iterator> - #include <sstream> - #include <string> -+#include <unistd.h> - - using namespace std; - diff --git a/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch b/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch deleted file mode 100644 index cb7dfb0..0000000 --- a/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch +++ /dev/null @@ -1,40 +0,0 @@ -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 - diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml deleted file mode 100644 index c0c84f0..0000000 --- a/sci-biology/abyss/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Haskell</name> - </maintainer> - <use> - <flag name='misc-haskell'>build abyss-samtobreak tool, pull in haskell toolchain</flag> - </use> -</pkgmetadata>
