* [gentoo-commits] proj/sci:master commit in: sci-biology/abyss/, sci-biology/abyss/files/
@ 2015-05-23 21:52 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2015-05-23 21:52 UTC (permalink / raw
To: gentoo-commits
commit: 4c3880bfe25f6b81461523e3f1f38b43614d51b9
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat May 23 21:51:58 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat May 23 21:51:58 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4c3880bf
sci-biology/amos: bring in upstream patch to cope with secondary alignments from 'bwa mem -M'
Package-Manager: portage-2.2.18
sci-biology/abyss/ChangeLog | 17 ++++++++
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 | 48 ++++++++++++++++++++++
.../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 | 5 +++
13 files changed, 360 insertions(+)
diff --git a/sci-biology/abyss/ChangeLog b/sci-biology/abyss/ChangeLog
new file mode 100644
index 0000000..c680959
--- /dev/null
+++ b/sci-biology/abyss/ChangeLog
@@ -0,0 +1,17 @@
+# ChangeLog for sci-biology/abyss
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*abyss-1.3.3-r1 (23 May 2015)
+*abyss-1.3.4-r1 (23 May 2015)
+*abyss-1.3.6-r1 (23 May 2015)
+
+ 23 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +abyss-1.3.3-r1.ebuild, +abyss-1.3.4-r1.ebuild, +abyss-1.3.6-r1.ebuild,
+ +files/abyss-1.3.3-ac_prog_ar.patch, +files/abyss-1.3.3-gcc-4.7.patch,
+ +files/abyss-1.3.3-samtoafg.patch, +files/abyss-1.3.4-gcc-4.7.patch,
+ +files/abyss-1.3.4-samtoafg.patch, +files/abyss-1.3.6-ac_prog_ar.patch,
+ +files/abyss-1.3.6-gcc-4.7.patch, +files/abyss-1.3.6-samtoafg.patch,
+ +metadata.xml:
+ sci-biology/amos: bring in upstream patch to cope with secondary alignments
+ from 'bwa mem -M'
diff --git a/sci-biology/abyss/abyss-1.3.3-r1.ebuild b/sci-biology/abyss/abyss-1.3.3-r1.ebuild
new file mode 100644
index 0000000..b727861
--- /dev/null
+++ b/sci-biology/abyss/abyss-1.3.3-r1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/abyss-1.3.3.ebuild,v 1.5 2013/08/11 14:55:22 jlec Exp $
+
+EAPI="4"
+
+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
new file mode 100644
index 0000000..48d7671
--- /dev/null
+++ b/sci-biology/abyss/abyss-1.3.4-r1.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/abyss-1.3.4.ebuild,v 1.3 2013/08/11 14:55:22 jlec Exp $
+
+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
new file mode 100644
index 0000000..d5d019e
--- /dev/null
+++ b/sci-biology/abyss/abyss-1.3.6-r1.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/abyss-1.3.6.ebuild,v 1.2 2014/07/06 11:12:45 jlec Exp $
+
+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/${P}.tar.gz"
+
+LICENSE="abyss"
+SLOT="0"
+IUSE="+mpi openmp"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+ dev-cpp/sparsehash
+ dev-libs/boost
+ mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+# 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() {
+ 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
new file mode 100644
index 0000000..300868f
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch
@@ -0,0 +1,18 @@
+ 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
new file mode 100644
index 0000000..42066f7
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch
@@ -0,0 +1,15 @@
+ 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
new file mode 100644
index 0000000..cb7dfb0
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.3.3-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
+
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
new file mode 100644
index 0000000..c2cc35c
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch
@@ -0,0 +1,15 @@
+ 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
new file mode 100644
index 0000000..cb7dfb0
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.3.4-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 $flag & 0x80; #FREAD2
+
diff --git a/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch
new file mode 100644
index 0000000..158e9b1
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch
@@ -0,0 +1,18 @@
+ configure.ac | 4 ++++
+ 1 file changed, 4 insertions(+)
+
+diff --git a/configure.ac b/configure.ac
+index 9d4bb66..aa94364 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -12,6 +12,10 @@ AC_PROG_CPP
+ AC_PROG_CXX
+ AC_PROG_INSTALL
+ AC_PROG_RANLIB
++AN_MAKEVAR([AR], [AC_PROG_AR])
++AN_PROGRAM([ar], [AC_PROG_AR])
++AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)])
++AC_PROG_AR
+ AC_CHECK_TOOL(GHC, ghc)
+ AM_CONDITIONAL([HAVE_GHC], [test "$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
new file mode 100644
index 0000000..c2cc35c
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch
@@ -0,0 +1,15 @@
+ 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
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
+
diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml
new file mode 100644
index 0000000..f17a827
--- /dev/null
+++ b/sci-biology/abyss/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/abyss/, sci-biology/abyss/files/
@ 2016-06-30 22:03 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2016-06-30 22:03 UTC (permalink / raw
To: gentoo-commits
commit: 76c8aa5fabb5f1ae43d4fdf831bcf94b7e6e09a6
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 30 22:02:59 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 30 22:02:59 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=76c8aa5f
sci-biology/abyss: version bump, update SRC_URI
Package-Manager: portage-2.2.28
sci-biology/abyss/abyss-1.9.0.ebuild | 52 ++++++++++++++++++++++
.../abyss/files/abyss-1.9.0-ac_prog_ar.patch | 18 ++++++++
sci-biology/abyss/metadata.xml | 15 +++++++
3 files changed, 85 insertions(+)
diff --git a/sci-biology/abyss/abyss-1.9.0.ebuild b/sci-biology/abyss/abyss-1.9.0.ebuild
new file mode 100644
index 0000000..b2de141
--- /dev/null
+++ b/sci-biology/abyss/abyss-1.9.0.ebuild
@@ -0,0 +1,52 @@
+# 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="https://github.com/bcgsc/abyss/archive/1.9.0.tar.gz -> ${P}.tar.gz"
+
+LICENSE="abyss"
+SLOT="0"
+IUSE="+mpi openmp misc-haskell"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-cpp/sparsehash
+ dev-libs/boost
+ misc-haskell? ( dev-libs/gmp:0=
+ virtual/libffi:0=
+ )
+ mpi? ( virtual/mpi )
+"
+DEPEND="${RDEPEND}
+ misc-haskell? ( dev-lang/ghc
+ dev-haskell/mmap )
+"
+
+# todo: --enable-maxk=N configure option
+# todo: fix automagic mpi toggling
+
+PATCHES=(
+ "${FILESDIR}"/${P}-ac_prog_ar.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 $(use_enable openmp)
+}
diff --git a/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch
new file mode 100644
index 0000000..158e9b1
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch
@@ -0,0 +1,18 @@
+ configure.ac | 4 ++++
+ 1 file changed, 4 insertions(+)
+
+diff --git a/configure.ac b/configure.ac
+index 9d4bb66..aa94364 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -12,6 +12,10 @@ AC_PROG_CPP
+ AC_PROG_CXX
+ AC_PROG_INSTALL
+ AC_PROG_RANLIB
++AN_MAKEVAR([AR], [AC_PROG_AR])
++AN_PROGRAM([ar], [AC_PROG_AR])
++AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)])
++AC_PROG_AR
+ AC_CHECK_TOOL(GHC, ghc)
+ AM_CONDITIONAL([HAVE_GHC], [test "$GHC"])
+
diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml
new file mode 100644
index 0000000..c0c84f0
--- /dev/null
+++ b/sci-biology/abyss/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>haskell@gentoo.org</email>
+ <name>Gentoo Haskell</name>
+ </maintainer>
+ <use>
+ <flag name='misc-haskell'>build abyss-samtobreak tool, pull in haskell toolchain</flag>
+ </use>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/abyss/, sci-biology/abyss/files/
@ 2017-01-10 0:20 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2017-01-10 0:20 UTC (permalink / raw
To: gentoo-commits
commit: 1ee6452972e294f0825ef450ec0f53cda42cb65f
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 10 00:20:33 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 10 00:20:33 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1ee64529
sci-biology/abyss: removing old, 2.0.2 in main repo already
sci-biology/abyss/abyss-1.9.0.ebuild | 53 ----------------------
.../abyss/files/abyss-1.9.0-ac_prog_ar.patch | 18 --------
sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch | 34 --------------
sci-biology/abyss/metadata.xml | 15 ------
4 files changed, 120 deletions(-)
diff --git a/sci-biology/abyss/abyss-1.9.0.ebuild b/sci-biology/abyss/abyss-1.9.0.ebuild
deleted file mode 100644
index c32b477..0000000
--- a/sci-biology/abyss/abyss-1.9.0.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# 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="https://github.com/bcgsc/abyss/archive/1.9.0.tar.gz -> ${P}.tar.gz"
-
-LICENSE="abyss"
-SLOT="0"
-IUSE="+mpi openmp misc-haskell"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-cpp/sparsehash
- dev-libs/boost
- misc-haskell? ( dev-libs/gmp:0=
- virtual/libffi:0=
- )
- mpi? ( virtual/mpi )
-"
-DEPEND="${RDEPEND}
- misc-haskell? ( dev-lang/ghc
- dev-haskell/mmap )
-"
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-PATCHES=(
- "${FILESDIR}"/${P}-ac_prog_ar.patch
- "${FILESDIR}"/${P}-gcc-6.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 $(use_enable openmp)
-}
diff --git a/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch
deleted file mode 100644
index 158e9b1..0000000
--- a/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch
+++ /dev/null
@@ -1,18 +0,0 @@
- configure.ac | 4 ++++
- 1 file changed, 4 insertions(+)
-
-diff --git a/configure.ac b/configure.ac
-index 9d4bb66..aa94364 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -12,6 +12,10 @@ AC_PROG_CPP
- AC_PROG_CXX
- AC_PROG_INSTALL
- AC_PROG_RANLIB
-+AN_MAKEVAR([AR], [AC_PROG_AR])
-+AN_PROGRAM([ar], [AC_PROG_AR])
-+AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)])
-+AC_PROG_AR
- AC_CHECK_TOOL(GHC, ghc)
- AM_CONDITIONAL([HAVE_GHC], [test "$GHC"])
-
diff --git a/sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch b/sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch
deleted file mode 100644
index 49a30f9..0000000
--- a/sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-diff --git a/DataBase/db-csv.cc b/DataBase/db-csv.cc
-index 05cac19..48e3b44 100644
---- a/DataBase/db-csv.cc
-+++ b/DataBase/db-csv.cc
-@@ -18,11 +18,11 @@ static const char TABLE_LIST[] =
- typedef vector<string> vs;
-
- static bool existFile(const char* f)
- {
- ifstream file(f);
-- return file;
-+ return bool(file);
- }
-
- template <typename D>
- static bool existTable(
- D& db, const string& t)
-diff --git a/SimpleGraph/SimpleGraph.cpp b/SimpleGraph/SimpleGraph.cpp
-index 373ec70..0a9ebd3 100644
---- a/SimpleGraph/SimpleGraph.cpp
-+++ b/SimpleGraph/SimpleGraph.cpp
-@@ -645,11 +645,11 @@ static void* worker(void* pArg)
- for (;;) {
- /** Lock the input stream. */
- static pthread_mutex_t inMutex = PTHREAD_MUTEX_INITIALIZER;
- pthread_mutex_lock(&inMutex);
- EstimateRecord er;
-- bool good = (*arg.in) >> er;
-+ bool good = bool((*arg.in) >> er);
- pthread_mutex_unlock(&inMutex);
- if (!good)
- break;
-
- // Flip the anterior distance estimates.
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>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <maintainer type="project">
- <email>haskell@gentoo.org</email>
- <name>Gentoo Haskell</name>
- </maintainer>
- <use>
- <flag name='misc-haskell'>build abyss-samtobreak tool, pull in haskell toolchain</flag>
- </use>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/abyss/, sci-biology/abyss/files/
@ 2021-04-14 13:07 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2021-04-14 13:07 UTC (permalink / raw
To: gentoo-commits
commit: f22bb3be4e8f283831edc5f4c38a839442355644
Author: Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Wed Apr 14 13:07:12 2021 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Apr 14 13:07:12 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f22bb3be
sci-biology/abyss: fix PathConsensus crashes
Fixes: https://github.com/bcgsc/abyss/issues/267
Fix crashes of PathConsensus during long-scaffolding
step per @sjackman suggestions.
Add back 2.2.5 version which does not have yet the
RResolver which addition broke the paired de Bruijn
graph assembly approach and since that only the
Bloom filter-based approach works in 2.3.0.
Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>
.../abyss/{abyss-2.3.0.ebuild => abyss-2.2.5-r1.ebuild} | 4 ++++
.../abyss/{abyss-2.3.0.ebuild => abyss-2.3.0-r1.ebuild} | 4 ++++
sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch | 11 +++++++++++
.../abyss/files/abyss-2.2.5-PathConsensus-assert.patch | 11 +++++++++++
4 files changed, 30 insertions(+)
diff --git a/sci-biology/abyss/abyss-2.3.0.ebuild b/sci-biology/abyss/abyss-2.2.5-r1.ebuild
similarity index 91%
copy from sci-biology/abyss/abyss-2.3.0.ebuild
copy to sci-biology/abyss/abyss-2.2.5-r1.ebuild
index 95438d3b4..d9134813b 100644
--- a/sci-biology/abyss/abyss-2.3.0.ebuild
+++ b/sci-biology/abyss/abyss-2.2.5-r1.ebuild
@@ -27,6 +27,10 @@ DEPEND="${RDEPEND}
dev-lang/ghc
)"
+PATCHES=( "${FILESDIR}"/${PN}-2.2.5-PathConsensus-assert.patch
+ "${FILESDIR}"/${PN}-2.2.5-ContigProperties.h.patch
+ )
+
# todo: --enable-maxk=N configure option
# todo: fix automagic mpi toggling
diff --git a/sci-biology/abyss/abyss-2.3.0.ebuild b/sci-biology/abyss/abyss-2.3.0-r1.ebuild
similarity index 91%
rename from sci-biology/abyss/abyss-2.3.0.ebuild
rename to sci-biology/abyss/abyss-2.3.0-r1.ebuild
index 95438d3b4..d9134813b 100644
--- a/sci-biology/abyss/abyss-2.3.0.ebuild
+++ b/sci-biology/abyss/abyss-2.3.0-r1.ebuild
@@ -27,6 +27,10 @@ DEPEND="${RDEPEND}
dev-lang/ghc
)"
+PATCHES=( "${FILESDIR}"/${PN}-2.2.5-PathConsensus-assert.patch
+ "${FILESDIR}"/${PN}-2.2.5-ContigProperties.h.patch
+ )
+
# todo: --enable-maxk=N configure option
# todo: fix automagic mpi toggling
diff --git a/sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch b/sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch
new file mode 100644
index 000000000..95181f082
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch
@@ -0,0 +1,11 @@
+--- abyss-2.2.5/Common/ContigProperties.h.ori 2020-09-18 20:42:12.000000000 +0200
++++ abyss-2.2.5/Common/ContigProperties.h 2021-04-14 12:31:23.682158000 +0200
+@@ -171,7 +171,7 @@
+ template <typename T>
+ ContigProperties& operator+=(ContigProperties& a, const T& b)
+ {
+- assert((int)a.length + (int)b.distance > 0);
++ assert((int)a.length + (int)b.distance >= 0);
+ a.length += b.distance;
+ return a;
+ }
diff --git a/sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch b/sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch
new file mode 100644
index 000000000..754e25acc
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch
@@ -0,0 +1,11 @@
+--- abyss-2.2.5/MergePaths/PathConsensus.cpp 2020-09-18 20:42:12.000000000 +0200
++++ abyss-2.2.5/MergePaths/PathConsensus.cpp 2021-04-12 22:26:28.780547000 +0200
+@@ -379,7 +379,7 @@
+ unsigned overlap, Sequence& seq,
+ const Sequence& s, const ContigNode& node, const Path& path)
+ {
+- assert(s.length() > overlap);
++ assert(s.length() >= overlap);
+ Sequence ao;
+ Sequence bo(s, 0, overlap);
+ Sequence o;
^ permalink raw reply related [flat|nested] 4+ messages in thread
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