14 files changed, 363 insertions, 0 deletions
diff --git a/sci-biology/abyss/ChangeLog b/sci-biology/abyss/ChangeLog
new file mode 100644
index 000000000..c6809596c
--- /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/Manifest b/sci-biology/abyss/Manifest
new file mode 100644
index 000000000..77dfde1ec
--- /dev/null
+++ b/sci-biology/abyss/Manifest
@@ -0,0 +1,3 @@
+DIST abyss-1.3.3.tar.gz 621480 SHA256 60396e2c8813952ceb1c66a3ad7c87eda984aa1e4952a14265217d9f639706a0 SHA512 4ec7fdd24bdb1e3d66e2bda50929122ff347107010701703e81ca1609fb1b4913c713991b3fe84a48ccfbc069e126f4f4120aafbab81e54e567a95a2f1099fb2 WHIRLPOOL 35f6fdfe60b70316e67bcbbb0a9c67e952302333e9ec71d893f2de7a94482dca1a604dc8cfef1ecee49e464244bb5df7469a8ad7bdc37bd54ff455b0f75b7914
+DIST abyss-1.3.4.tar.gz 640545 SHA256 6b6ccb04baaa9d244dd67d95e1512a934d2e54fd28a539149b6845ed5c496baf SHA512 0fa4c14117699945e007412deaeeccca27124a210669accbc1444baf5a4de1a17e1f9b48e6ee43fefed63f0d56b933c847363e59a0fc2bad60ae6d603cd8c09e WHIRLPOOL 42b16f22bc47c8f29b07c256d504d6f58119c64fdcf0e198fd8b836ceb45139fd5cadc7feec72adf958800e55eb1065a449ce7dd288339887dcea4ab13623c01
+DIST abyss-1.3.6.tar.gz 678880 SHA256 4432a8b5046bdcb548b6f1b22069a6cade4dea26fc6f83ad5467548e4f3e7c95 SHA512 2c6d72e0227c4af2d5740a989168ad35a84b9236dc53b65a29a010c4e5f77e5c4bfaa38bfaa2f14fd530ae6df204294ff167bd40e79f61e8bad6a7489bf34ace WHIRLPOOL 0677b1fd4090ba155fb876c0047a1ccd2ec2e220950e1e9940e1f3df05ef0abd3ba2e3dbabd500d6fab39a8f7d94e02e0a07410934733682a70fa605d2a8bc07
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 000000000..b7278619c
--- /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 000000000..48d767122
--- /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 000000000..d5d019eca
--- /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 000000000..300868f52
--- /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 000000000..42066f7f2
--- /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 000000000..cb7dfb08a
--- /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 000000000..c2cc35c31
--- /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 000000000..cb7dfb08a
--- /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 $flag & 0x80; #FREAD2
+ 
diff --git a/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch
new file mode 100644
index 000000000..158e9b126
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch
@@ -0,0 +1,18 @@
+ configure.ac | 4 ++++
+ 1 file changed, 4 insertions(+)
+
+diff --git a/configure.ac b/configure.ac
+index 9d4bb66..aa94364 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -12,6 +12,10 @@ AC_PROG_CPP
+ AC_PROG_CXX
+ AC_PROG_INSTALL
+ AC_PROG_RANLIB
++AN_MAKEVAR([AR], [AC_PROG_AR])
++AN_PROGRAM([ar], [AC_PROG_AR])
++AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)])
++AC_PROG_AR
+ AC_CHECK_TOOL(GHC, ghc)
+ AM_CONDITIONAL([HAVE_GHC], [test "$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 000000000..c2cc35c31
--- /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 000000000..cb7dfb08a
--- /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 000000000..f17a827e3
--- /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>