13 files changed, 0 insertions, 367 deletions
diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest
deleted file mode 100644
index 77dfde1ec..000000000
--- a/sci-biology/abyss/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-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
deleted file mode 100644
index 76f15b496..000000000
--- 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 762d49a79..000000000
--- 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 a449c72dc..000000000
--- 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 300868f52..000000000
--- 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 42066f7f2..000000000
--- 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 cb7dfb08a..000000000
--- 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 c2cc35c31..000000000
--- 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 cb7dfb08a..000000000
--- 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 $flag & 0x80; #FREAD2
- 
diff --git a/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch
deleted file mode 100644
index 158e9b126..000000000
--- a/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch
+++ /dev/null
@@ -1,18 +0,0 @@
- configure.ac | 4 ++++
- 1 file changed, 4 insertions(+)
-
-diff --git a/configure.ac b/configure.ac
-index 9d4bb66..aa94364 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -12,6 +12,10 @@ AC_PROG_CPP
- AC_PROG_CXX
- AC_PROG_INSTALL
- AC_PROG_RANLIB
-+AN_MAKEVAR([AR], [AC_PROG_AR])
-+AN_PROGRAM([ar], [AC_PROG_AR])
-+AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)])
-+AC_PROG_AR
- AC_CHECK_TOOL(GHC, ghc)
- AM_CONDITIONAL([HAVE_GHC], [test "$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 c2cc35c31..000000000
--- 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 cb7dfb08a..000000000
--- 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 c0c84f0ed..000000000
--- 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>