commit: 2778b51209c924509c1dfcdf68d505b78f7654a1
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 21 19:07:06 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 21 19:14:06 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2778b512
sci-biology/jellyfish: SLOT jellyfish to support concurrent ver. {1,2}
This renames the resulting binaries, pkg-config file contents, headers, and all
packages currently depending on sci-biology/jellyfish.
sci-biology/quorum: SLOT jellyfish to support concurrent ver. {1,2}
sci-biology/Rcorrector: SLOT jellyfish to support concurrent ver. {1,2}
sci-biology/SEECER: SLOT jellyfish to support concurrent ver. {1,2}
sci-biology/amos: SLOT jellyfish to support concurrent ver. {1,2}
sci-biology/kraken: SLOT jellyfish to support concurrent ver. {1,2}
sci-biology/wgs-assembler: SLOT jellyfish to support concurrent ver. {1,2}
Package-Manager: Portage-2.3.28, Repoman-2.3.9
sci-biology/Rcorrector/Rcorrector-9999.ebuild | 14 ++--
.../files/Rcorrector-rename-jellyfish.patch | 36 +++++++++++
sci-biology/SEECER/SEECER-0.1.3-r2.ebuild | 4 +-
.../SEECER/files/remove-hardcoded-paths.patch | 2 +-
.../SEECER/files/rename_jellyfish_binary.patch | 2 +-
sci-biology/amos/amos-3.1.0-r2.ebuild | 4 +-
sci-biology/amos/amos-9999.ebuild | 2 +-
...1.1.11-r1.ebuild => jellyfish-1.1.11-r2.ebuild} | 18 ++++--
...fish-2.1.4.ebuild => jellyfish-2.1.3-r1.ebuild} | 13 ++--
...fish-2.1.3.ebuild => jellyfish-2.1.4-r1.ebuild} | 13 ++--
...fish-2.2.6.ebuild => jellyfish-2.2.6-r1.ebuild} | 13 ++--
sci-biology/kraken/kraken-1.0.ebuild | 7 +-
.../quorum/files/quorum-0.2.1-use-jellyfish1.patch | 74 ++++++++++++++++++++++
...{quorum-0.2.1.ebuild => quorum-0.2.1-r1.ebuild} | 15 +++--
sci-biology/quorum/quorum-1.1.1.ebuild | 4 +-
.../wgs-assembler-8.3_rc2-rename-jellyfish.patch | 69 ++++++++++++++++++++
.../wgs-assembler/wgs-assembler-8.3_rc2.ebuild | 12 ++--
17 files changed, 255 insertions(+), 47 deletions(-)
diff --git a/sci-biology/Rcorrector/Rcorrector-9999.ebuild
b/sci-biology/Rcorrector/Rcorrector-9999.ebuild
index 71f6dd45e..58007a73b 100644
--- a/sci-biology/Rcorrector/Rcorrector-9999.ebuild
+++ b/sci-biology/Rcorrector/Rcorrector-9999.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=6
-inherit git-r3
+inherit git-r3 eutils
DESCRIPTION="Error correction for Illumina RNA-seq reads"
HOMEPAGE="https://github.com/mourisl/Rcorrector";
@@ -15,14 +15,16 @@ SLOT="0"
KEYWORDS=""
IUSE=""
-DEPEND=">=sci-biology/jellyfish-2.1.3"
+DEPEND=">=sci-biology/jellyfish-2.1.3:2"
RDEPEND="${DEPEND}
dev-lang/perl"
src_prepare(){
+ default
+ epatch "${FILESDIR}"/Rcorrector-rename-jellyfish.patch
# prevent building of jellyfish from bundled sources
- mkdir -p jellyfish-2.1.3/bin
- touch jellyfish-2.1.3/bin/jellyfish
+ mkdir -p ./jellyfish/bin/ || die
+ touch ./jellyfish/bin/jellyfish2 || die
sed -e "s#-Wall -O3#${CXXFLAGS}#" -i Makefile || die
}
diff --git a/sci-biology/Rcorrector/files/Rcorrector-rename-jellyfish.patch
b/sci-biology/Rcorrector/files/Rcorrector-rename-jellyfish.patch
new file mode 100644
index 000000000..08b9918d4
--- /dev/null
+++ b/sci-biology/Rcorrector/files/Rcorrector-rename-jellyfish.patch
@@ -0,0 +1,36 @@
+--- Makefile.ori 2018-04-21 17:47:38.017147315 +0200
++++ Makefile 2018-04-21 17:48:29.038679685 +0200
+@@ -2,14 +2,14 @@
+ CXXFLAGS= -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize
-std=c++0x
+ LINKFLAGS = -I . -lpthread -lz
+ DEBUG=
+-jellyfishPath = `which jellyfish`
+-jellyfishVersion = `jellyfish --version | cut -f2 -d' ' | cut -f1 -d'.'`
++jellyfishPath = `which jellyfish2`
++jellyfishVersion = `jellyfish2 --version | cut -f2 -d' ' | cut -f1 -d'.'`
+ OBJECTS = KmerCode.o ErrorCorrection.o
+ all: main.o $(OBJECTS)
+ $(CXX) -o rcorrector $(CXXFLAGS) $(OBJECTS) main.o $(LINKFLAGS)
+ if [ ! $(jellyfishPath) ] || [ $(jellyfishVersion) -ne 2 ] ; \
+ then \
+- if [ ! -f ./jellyfish/bin/jellyfish ] ; \
++ if [ ! -f ./jellyfish/bin/jellyfish2 ] ; \
+ then \
+ wget -O jellyfish.tar.gz
https://github.com/gmarcais/Jellyfish/releases/download/v2.2.4/jellyfish-2.2.4.tar.gz
;\
+ tar -xzf jellyfish.tar.gz ; mv jellyfish-2.2.4
jellyfish ; rm jellyfish.tar.gz ; cd jellyfish && ./configure && make ;\
+--- run_rcorrector.pl.ori 2018-04-21 17:48:43.459112787 +0200
++++ run_rcorrector.pl 2018-04-21 17:49:18.070152287 +0200
+@@ -42,10 +42,10 @@
+ die "$usage\n" ;
+ }
+
+-my $jellyfishBin = "jellyfish" ;
+-if ( -e "$WD/jellyfish/bin/jellyfish" )
++my $jellyfishBin = "jellyfish2" ;
++if ( -e "$WD/jellyfish/bin/jellyfish2" )
+ {
+- $jellyfishBin = "$WD/jellyfish/bin/jellyfish" ;
++ $jellyfishBin = "$WD/jellyfish/bin/jellyfish2" ;
+ }
+
+ my $fileArguments ;
diff --git a/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild
b/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild
index 0b7ec3bfa..49ebd3879 100644
--- a/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild
+++ b/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -22,7 +22,7 @@ DEPEND="
sci-libs/gsl:0=
sci-biology/seqan:0="
RDEPEND="${DEPEND}
- =sci-biology/jellyfish-1.1.11-r1"
+ sci-biology/jellyfish:1"
S="${S}"/SEECER
diff --git a/sci-biology/SEECER/files/remove-hardcoded-paths.patch
b/sci-biology/SEECER/files/remove-hardcoded-paths.patch
index bb46f6a30..6583ee47d 100644
--- a/sci-biology/SEECER/files/remove-hardcoded-paths.patch
+++ b/sci-biology/SEECER/files/remove-hardcoded-paths.patch
@@ -42,7 +42,7 @@
-BINDIR='bin/' #this can be hardcoded to /absolute/path/to/SEECER/bin/
-JF="../jellyfish-1.1.11/bin/jellyfish" #this may be hardcoded to
/absolute/path/to/jellyfish/bin/
+BINDIR='' #this can be hardcoded to /absolute/path/to/SEECER/bin/
-+JF="jellyfish" #this may be hardcoded to /absolute/path/to/jellyfish/bin/
++JF="jellyfish1" #this may be hardcoded to /absolute/path/to/jellyfish/bin/
K=17
SEECER_PARAMS=""
diff --git a/sci-biology/SEECER/files/rename_jellyfish_binary.patch
b/sci-biology/SEECER/files/rename_jellyfish_binary.patch
index c6548cee1..d4fd3b0a7 100644
--- a/sci-biology/SEECER/files/rename_jellyfish_binary.patch
+++ b/sci-biology/SEECER/files/rename_jellyfish_binary.patch
@@ -4,7 +4,7 @@
BINDIR='' #this can be hardcoded to /absolute/path/to/SEECER/bin/
--JF="jellyfish" #this may be hardcoded to /absolute/path/to/jellyfish/bin/
+-JF="jellyfish1" #this may be hardcoded to /absolute/path/to/jellyfish/bin/
+JF="jellyfish1" #this may be hardcoded to
/absolute/path/to/jellyfish/bin/jellyfish
K=17
diff --git a/sci-biology/amos/amos-3.1.0-r2.ebuild
b/sci-biology/amos/amos-3.1.0-r2.ebuild
index c4753c36e..d4107d509 100644
--- a/sci-biology/amos/amos-3.1.0-r2.ebuild
+++ b/sci-biology/amos/amos-3.1.0-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -24,7 +24,7 @@ DEPEND="
qt4? ( dev-qt/qtcore:4[qt3support]
dev-qt/qt3support:4 )
sci-biology/blat
- sci-biology/jellyfish"
+ sci-biology/jellyfish:1"
RDEPEND="${DEPEND}
dev-lang/perl
dev-perl/DBI
diff --git a/sci-biology/amos/amos-9999.ebuild
b/sci-biology/amos/amos-9999.ebuild
index 2c911603d..55eb97e1a 100644
--- a/sci-biology/amos/amos-9999.ebuild
+++ b/sci-biology/amos/amos-9999.ebuild
@@ -27,7 +27,7 @@ DEPEND="
qt4? ( dev-qt/qtcore:4[qt3support]
dev-qt/qt3support:4 )
sci-biology/blat
- sci-biology/jellyfish"
+ sci-biology/jellyfish:1"
RDEPEND="${DEPEND}
dev-perl/DBI
dev-perl/Statistics-Descriptive
diff --git a/sci-biology/jellyfish/jellyfish-1.1.11-r1.ebuild
b/sci-biology/jellyfish/jellyfish-1.1.11-r2.ebuild
similarity index 68%
rename from sci-biology/jellyfish/jellyfish-1.1.11-r1.ebuild
rename to sci-biology/jellyfish/jellyfish-1.1.11-r2.ebuild
index 923784ada..a9b0ce4d1 100644
--- a/sci-biology/jellyfish/jellyfish-1.1.11-r1.ebuild
+++ b/sci-biology/jellyfish/jellyfish-1.1.11-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -15,7 +15,7 @@
SRC_URI="http://www.cbcb.umd.edu/software/jellyfish/jellyfish-1.1.11.tar.gz
# also bundled in SEECER-0.1.3
LICENSE="GPL-3+ BSD"
-SLOT="0"
+SLOT="1"
KEYWORDS="~amd64 ~x86"
IUSE="cpu_flags_x86_sse"
@@ -34,11 +34,15 @@ src_prepare(){
}
src_install(){
- # install the binary under jellyfish1 name like Debian/Ubuntu to avoid
name clash with jellyfish2 and allow simultaneous installs
- mv bin/jellyfish bin/jellyfish1 || die
default
- sed -e "s#jellyfish-${PV}#jellyfish#" -i
"${ED}/usr/$(get_libdir)"/pkgconfig/jellyfish-1.1.pc || die
- mkdir -p "${ED}/usr/include/${PN}" || die
- mv "${ED}"/usr/include/"${P}"/"${PN}"/* "${ED}/usr/include/${PN}/" ||
die
+ # install the binary under jellyfish1 name like Debian/Ubuntu to avoid
name clash with jellyfish2 and allow simultaneous installs
+ mv "${ED}"/usr/bin/jellyfish "${ED}"/usr/bin/jellyfish1 || die
+ sed -e "s#jellyfish-${PV}#jellyfish1#" -i
"${ED}/usr/$(get_libdir)"/pkgconfig/jellyfish-1.1.pc || die
+ find "${ED}"/usr/include/"${P}"/"${PN}" -type f | while read f; do
+ sed -e "s#include <jellyfish/#include <jellyfish${SLOT}/#" -i
$f || die
+ done
+ mkdir -p "${ED}/usr/include/${PN}${SLOT}" || die
+ mv "${ED}"/usr/include/"${P}"/"${PN}"/*
"${ED}/usr/include/${PN}${SLOT}/" || die
rm -r "${ED}/usr/include/${P}" || die
+ mv "${ED}"/usr/share/man/man1/jellyfish.1
"${ED}"/usr/share/man/man1/jellyfish"${SLOT}".1 || die
}
diff --git a/sci-biology/jellyfish/jellyfish-2.1.4.ebuild
b/sci-biology/jellyfish/jellyfish-2.1.3-r1.ebuild
similarity index 70%
rename from sci-biology/jellyfish/jellyfish-2.1.4.ebuild
rename to sci-biology/jellyfish/jellyfish-2.1.3-r1.ebuild
index fd71046ac..115848f30 100644
--- a/sci-biology/jellyfish/jellyfish-2.1.4.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.1.3-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -13,7 +13,7 @@ SRC_URI="ftp://ftp.genome.umd.edu/pub/${PN}/${P}.tar.gz
# older version is hidden in
trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
LICENSE="GPL-3+ BSD"
-SLOT="0"
+SLOT="2"
KEYWORDS="~amd64 ~x86"
IUSE="cpu_flags_x86_sse"
@@ -33,8 +33,13 @@ src_prepare(){
src_install(){
default
+ mv "${ED}"/usr/bin/jellyfish "${ED}"/usr/bin/jellyfish2 || die
sed -e "s#jellyfish-${PV}#jellyfish#" -i
"${ED}/usr/$(get_libdir)"/pkgconfig/jellyfish-2.0.pc || die
- mkdir -p "${ED}/usr/include/${PN}" || die
- mv "${ED}"/usr/include/"${P}"/"${PN}"/* "${ED}/usr/include/${PN}/" ||
die
+ find "${ED}"/usr/include/"${P}"/"${PN}" -type f | while read f; do
+ sed -e "s#include <jellyfish/#include <jellyfish${SLOT}/#" -i $f || die
+ done
+ mkdir -p "${ED}/usr/include/${PN}${SLOT}" || die
+ mv "${ED}"/usr/include/"${P}"/"${PN}"/*
"${ED}/usr/include/${PN}${SLOT}/" || die
rm -r "${ED}/usr/include/${P}" || die
+ mv "${ED}"/usr/share/man/man1/jellyfish.1
"${ED}"/usr/share/man/man1/jellyfish"${SLOT}".1 || die
}
diff --git a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
b/sci-biology/jellyfish/jellyfish-2.1.4-r1.ebuild
similarity index 70%
rename from sci-biology/jellyfish/jellyfish-2.1.3.ebuild
rename to sci-biology/jellyfish/jellyfish-2.1.4-r1.ebuild
index fd71046ac..248e2cef4 100644
--- a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.1.4-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -13,7 +13,7 @@ SRC_URI="ftp://ftp.genome.umd.edu/pub/${PN}/${P}.tar.gz
# older version is hidden in
trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
LICENSE="GPL-3+ BSD"
-SLOT="0"
+SLOT="2"
KEYWORDS="~amd64 ~x86"
IUSE="cpu_flags_x86_sse"
@@ -33,8 +33,13 @@ src_prepare(){
src_install(){
default
+ mv "${ED}"/usr/bin/jellyfish "${ED}"/usr/bin/jellyfish2 || die
sed -e "s#jellyfish-${PV}#jellyfish#" -i
"${ED}/usr/$(get_libdir)"/pkgconfig/jellyfish-2.0.pc || die
- mkdir -p "${ED}/usr/include/${PN}" || die
- mv "${ED}"/usr/include/"${P}"/"${PN}"/* "${ED}/usr/include/${PN}/" ||
die
+ find "${ED}"/usr/include/"${P}"/"${PN}" -type f | while read f; do
+ sed -e "s#include <jellyfish/#include <jellyfish${SLOT}/#" -i
$f || die
+ done
+ mkdir -p "${ED}/usr/include/${PN}${SLOT}" || die
+ mv "${ED}"/usr/include/"${P}"/"${PN}"/*
"${ED}/usr/include/${PN}${SLOT}/" || die
rm -r "${ED}/usr/include/${P}" || die
+ mv "${ED}"/usr/share/man/man1/jellyfish.1
"${ED}"/usr/share/man/man1/jellyfish"${SLOT}".1 || die
}
diff --git a/sci-biology/jellyfish/jellyfish-2.2.6.ebuild
b/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild
similarity index 74%
rename from sci-biology/jellyfish/jellyfish-2.2.6.ebuild
rename to sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild
index af91bd892..21b002b9c 100644
--- a/sci-biology/jellyfish/jellyfish-2.2.6.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -13,7 +13,7 @@
SRC_URI="https://github.com/gmarcais/Jellyfish/releases/download/v${PV}/${P}.tar
# older version is hidden in
trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
LICENSE="GPL-3+ BSD"
-SLOT="0"
+SLOT="2"
KEYWORDS="~amd64 ~x86"
IUSE="cpu_flags_x86_sse"
@@ -39,8 +39,13 @@ src_configure(){
src_install(){
default
+ mv "${ED}"/usr/bin/jellyfish "${ED}"/usr/bin/jellyfish2 || die
sed -e "s#jellyfish-${PV}#jellyfish#" -i
"${ED}/usr/$(get_libdir)"/pkgconfig/jellyfish-2.0.pc || die
- mkdir -p "${ED}/usr/include/${PN}" || die
- mv "${ED}"/usr/include/"${P}"/"${PN}"/* "${ED}/usr/include/${PN}/" ||
die
+ find "${ED}"/usr/include/"${P}"/"${PN}" -type f | while read f; do
+ sed -e "s#include <jellyfish/#include <jellyfish${SLOT}/#" -i
$f || die
+ done
+ mkdir -p "${ED}/usr/include/${PN}${SLOT}" || die
+ mv "${ED}"/usr/include/"${P}"/"${PN}"/*
"${ED}/usr/include/${PN}${SLOT}/" || die
rm -r "${ED}/usr/include/${P}" || die
+ mv "${ED}"/usr/share/man/man1/jellyfish.1
"${ED}"/usr/share/man/man1/jellyfish"${SLOT}".1 || die
}
diff --git a/sci-biology/kraken/kraken-1.0.ebuild
b/sci-biology/kraken/kraken-1.0.ebuild
index b579a7eef..efad890ce 100644
--- a/sci-biology/kraken/kraken-1.0.ebuild
+++ b/sci-biology/kraken/kraken-1.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -20,7 +20,8 @@ IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
dev-lang/perl
- net-misc/wget"
+ net-misc/wget
+ sci-biology/jellyfish:1"
src_prepare(){
sed -e 's/^CXX = /CXX ?= /' -e 's/^CXXFLAGS = /CXXFLAGS ?= /' -i
src/Makefile || die
@@ -32,7 +33,7 @@ src_compile(){
}
src_install(){
- dohtml "${DISTDIR}"/${P}_MANUAL.html
+ dodoc "${DISTDIR}"/${P}_MANUAL.html
perl_set_version
insinto ${VENDOR_LIB}/${PN}
doins destdir/*.pm
diff --git a/sci-biology/quorum/files/quorum-0.2.1-use-jellyfish1.patch
b/sci-biology/quorum/files/quorum-0.2.1-use-jellyfish1.patch
new file mode 100644
index 000000000..b5b68a8fb
--- /dev/null
+++ b/sci-biology/quorum/files/quorum-0.2.1-use-jellyfish1.patch
@@ -0,0 +1,74 @@
+--- src/error_correct_reads.cc 2018-04-21 14:25:41.310473159 +0200
++++ src/error_correct_reads.cc 2018-04-21 14:26:58.262493179 +0200
+@@ -25,9 +25,9 @@
+ #endif
+
+ //#define DEBUG 1
+-#include <jellyfish/dbg.hpp>
+-#include <jellyfish/atomic_gcc.hpp>
+-#include <jellyfish/mer_counting.hpp>
++#include <jellyfish1/dbg.hpp>
++#include <jellyfish1/atomic_gcc.hpp>
++#include <jellyfish1/mer_counting.hpp>
+
+ #include <jflib/multiplexed_io.hpp>
+ #include <gzip_stream.hpp>
+--- src/combine_jf_dbs.cc 2018-04-21 14:25:50.220707057 +0200
++++ src/combine_jf_dbs.cc 2018-04-21 14:27:04.652660923 +0200
+@@ -1,9 +1,9 @@
+-#include <jellyfish/err.hpp>
+-#include <jellyfish/misc.hpp>
+-#include <jellyfish/mer_counting.hpp>
+-#include <jellyfish/compacted_hash.hpp>
+-#include <jellyfish/thread_exec.hpp>
+-#include <jellyfish/misc.hpp>
++#include <jellyfish1/err.hpp>
++#include <jellyfish1/misc.hpp>
++#include <jellyfish1/mer_counting.hpp>
++#include <jellyfish1/compacted_hash.hpp>
++#include <jellyfish1/thread_exec.hpp>
++#include <jellyfish1/misc.hpp>
+ #include <src/combine_jf_dbs.hpp>
+
+ int main(int argc, char *argv[])
+--- src/error_correct_reads.hpp 2018-04-21 14:26:10.091228666 +0200
++++ src/error_correct_reads.hpp 2018-04-21 14:27:09.792795853 +0200
+@@ -2,12 +2,12 @@
+ #define __ERROR_CORRECT_READS_HPP__
+
+ #include <config.h>
+-#include <jellyfish/err.hpp>
+-#include <jellyfish/mapped_file.hpp>
+-#include <jellyfish/invertible_hash_array.hpp>
+-#include <jellyfish/allocators_mmap.hpp>
+-#include <jellyfish/parse_read.hpp>
+-#include <jellyfish/thread_exec.hpp>
++#include <jellyfish1/err.hpp>
++#include <jellyfish1/mapped_file.hpp>
++#include <jellyfish1/invertible_hash_array.hpp>
++#include <jellyfish1/allocators_mmap.hpp>
++#include <jellyfish1/parse_read.hpp>
++#include <jellyfish1/thread_exec.hpp>
+ #include <iostream>
+ #include <fstream>
+ #include <assert.h>
+--- configure.ac.ori 2018-04-21 15:00:35.225439196 +0200
++++ configure.ac 2018-04-21 15:01:37.977086449 +0200
+@@ -28,7 +28,7 @@
+ JELLYFISH_VERSION=$(pkg-config --modversion jellyfish-1.1)
+ AC_SUBST([JELLYFISH_VERSION])
+ AC_ARG_VAR([JELLYFISH], [Jellyfish executable absolute path (default to
looking in PATH)])
+-AS_IF([test "x$JELLYFISH" = "x"], [AC_PATH_PROG([JELLYFISH], [jellyfish],
[false])])
++AS_IF([test "x$JELLYFISH" = "x"], [AC_PATH_PROG([JELLYFISH], [jellyfish1],
[false])])
+
+ AC_ARG_VAR([JF_LIB_PATH], [Append this path to LD_LIBRARY_PATH in quorum])
+
+@@ -47,7 +47,7 @@
+ # --with-relative-jf-path
+ AC_ARG_WITH([relative-jf-path],
+ [AC_HELP_STRING([--with-relative-jf-path], [relative path from
quorum to jellyfish (use an absolute path if not given. default to "." if given
with no argument)])],
+- [case "$withval" in (yes) with_relative_jf_path="jellyfish" ;;
(no) with_relative_jf_path= ;; (*) with_relative_jf_path=$withval/jellyfish ;;
esac],
++ [case "$withval" in (yes) with_relative_jf_path="jellyfish1" ;;
(no) with_relative_jf_path= ;; (*) with_relative_jf_path=$withval/jellyfish1 ;;
esac],
+ [with_relative_jf_path= ])
+ AC_SUBST([RELATIVE_JF_PATH], $with_relative_jf_path)
+ AM_CONDITIONAL([HAVE_RELATIVE_JF_PATH], [test x$with_relative_jf_path != x])
diff --git a/sci-biology/quorum/quorum-0.2.1.ebuild
b/sci-biology/quorum/quorum-0.2.1-r1.ebuild
similarity index 66%
rename from sci-biology/quorum/quorum-0.2.1.ebuild
rename to sci-biology/quorum/quorum-0.2.1-r1.ebuild
index 58c4ae79e..d7bb7675a 100644
--- a/sci-biology/quorum/quorum-0.2.1.ebuild
+++ b/sci-biology/quorum/quorum-0.2.1-r1.ebuild
@@ -1,7 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=6
+
+inherit eutils autotools
DESCRIPTION="Correct substitution errors in Illumina reads"
HOMEPAGE="http://www.genome.umd.edu/quorum.html";
@@ -12,10 +14,15 @@ SLOT="0"
KEYWORDS="~amd64"
IUSE=""
-DEPEND=">=sci-biology/jellyfish-1.1.11
- <=sci-biology/jellyfish-2.0.0"
+DEPEND="sci-biology/jellyfish:1"
RDEPEND="${DEPEND}"
+src_prepare(){
+ default
+ epatch "${FILESDIR}"/"${P}"-use-jellyfish1.patch
+ eautoreconf
+}
+
src_configure(){
econf --enable-relative-paths --with-relative-jf-path
}
diff --git a/sci-biology/quorum/quorum-1.1.1.ebuild
b/sci-biology/quorum/quorum-1.1.1.ebuild
index 8a3ced37f..6fa222ff7 100644
--- a/sci-biology/quorum/quorum-1.1.1.ebuild
+++ b/sci-biology/quorum/quorum-1.1.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -13,7 +13,7 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
-DEPEND=">=sci-biology/jellyfish-2.1.4"
+DEPEND=">=sci-biology/jellyfish-2.1.4:2"
RDEPEND="${DEPEND}"
src_configure(){
diff --git
a/sci-biology/wgs-assembler/files/wgs-assembler-8.3_rc2-rename-jellyfish.patch
b/sci-biology/wgs-assembler/files/wgs-assembler-8.3_rc2-rename-jellyfish.patch
new file mode 100644
index 000000000..d98ba7b52
--- /dev/null
+++
b/sci-biology/wgs-assembler/files/wgs-assembler-8.3_rc2-rename-jellyfish.patch
@@ -0,0 +1,69 @@
+--- src/AS_PBR/PBcR.pl.ori 2015-05-20 23:28:27.000000000 +0200
++++ src/AS_PBR/PBcR.pl 2018-04-21 16:24:14.189313208 +0200
+@@ -1259,12 +1259,12 @@
+ setGlobal("mhap", undef);
+ }
+
+-if (! -e "$JELLYFISH/jellyfish") {
+- if (-e "$CA/jellyfish") {
++if (! -e "$JELLYFISH/jellyfish2") {
++ if (-e "$CA/jellyfish2") {
+ $JELLYFISH = $CA;
+ } else {
+ # try to use path
+- my $amosPath = `which jellyfish`;
++ my $amosPath = `which jellyfish2`;
+ chomp $amosPath;
+ my @t = split '/', "$amosPath";
+ pop @t; # blasr
+@@ -1698,7 +1698,7 @@
+ }
+
+ my $ignore = "";
+-if (!defined(getGlobal("bowtie")) && $cutoffSpecified == 0 &&
!(defined(getGlobal("mhap")) && -e "$JELLYFISH/jellyfish")) {
++if (!defined(getGlobal("bowtie")) && $cutoffSpecified == 0 &&
!(defined(getGlobal("mhap")) && -e "$JELLYFISH/jellyfish2")) {
+ # run correction up thorough meryl
+ if (! -e "$wrk/temp$libraryname/0-mercounts/$asm.nmers.ovl.fasta") {
+ $cmd = "$CA/runCA ";
+@@ -1740,20 +1740,20 @@
+ $inFile = `ls $wrk/*.$inMer.ignore |wc -l |awk '{print \$1}'`;
+ }
+ chomp $inFile;
+-if ($inFile == 0 && !-e "$wrk/temp$libraryname/$asm.ignore" && -e
"$JELLYFISH/jellyfish" && defined(getGlobal("mhap"))) {
++if ($inFile == 0 && !-e "$wrk/temp$libraryname/$asm.ignore" && -e
"$JELLYFISH/jellyfish2" && defined(getGlobal("mhap"))) {
+ my $f = makeAbsolute($fastqFile);
+ if ($f =~ /\.bz2$/i || $f =~ /\.zip$/i || $f =~ /\.gz$/i) {
+ die "Input fastq file $f is compressed. This is currently not
supported, please uncompress the file and try again.";
+ }
+- $cmd = "$JELLYFISH/jellyfish count ";
++ $cmd = "$JELLYFISH/jellyfish2 count ";
+ $cmd .= " -m " . getGlobal("merSize") . " -s 120000000 -t " .
getGlobal("merylThreads") . " -o $wrk/temp$libraryname/$asm.mers " .
makeAbsolute($fastqFile);
+ runCommand("$wrk/temp$libraryname", $cmd);
+ if ( -e "$wrk/temp$libraryname/$asm.mers_0") {
+- $cmd = "$JELLYFISH/jellyfish merge -s 120000000 -o
$wrk/temp$libraryname/$asm.mers $wrk/temp$libraryname/$asm.mers_*";
++ $cmd = "$JELLYFISH/jellyfish2 merge -s 120000000 -o
$wrk/temp$libraryname/$asm.mers $wrk/temp$libraryname/$asm.mers_*";
+ runCommand("$wrk/temp$libraryname", $cmd);
+ }
+
+- $cmd = "$JELLYFISH/jellyfish histo -t " . getGlobal("merylThreads") . "
-f $wrk/temp$libraryname/$asm.mers > $wrk/temp$libraryname/$asm.hist";
++ $cmd = "$JELLYFISH/jellyfish2 histo -t " . getGlobal("merylThreads") . "
-f $wrk/temp$libraryname/$asm.mers > $wrk/temp$libraryname/$asm.hist";
+ runCommand("$wrk/temp$libraryname", $cmd);
+ my $total = 0;
+ my $runningSum = 0;
+@@ -1763,7 +1763,7 @@
+ chomp $cut;
+ $cut++;
+
+- $cmd = "$JELLYFISH/jellyfish dump -c -t -L $cut
$wrk/temp$libraryname/$asm.mers |awk -v TOTAL=$sum
'{printf(\"\%s\\t\%0.10f\\t\%d\\t\%d\\n\", \$1, \$2/TOTAL, \$2, TOTAL)}' |sort
-T . -rnk2> $wrk/temp$libraryname/$asm.ignore";
++ $cmd = "$JELLYFISH/jellyfish2 dump -c -t -L $cut
$wrk/temp$libraryname/$asm.mers |awk -v TOTAL=$sum
'{printf(\"\%s\\t\%0.10f\\t\%d\\t\%d\\n\", \$1, \$2/TOTAL, \$2, TOTAL)}' |sort
-T . -rnk2> $wrk/temp$libraryname/$asm.ignore";
+ runCommand("$wrk/temp$libraryname", $cmd);
+ runCommand("$wrk/temp$libraryname", "rm $wrk/temp$libraryname/$asm.mers*");
+ } elsif (!-e "$wrk/temp$libraryname/$asm.ignore" &&
defined(getGlobal("mhap"))) {
+--- src/AS_PBR/Makefile.ori 2015-02-20 23:54:49.000000000 +0100
++++ src/AS_PBR/Makefile 2018-04-21 16:24:50.730272421 +0200
+@@ -222,4 +222,4 @@
+ @echo "!!!!!!! WARNING pbutgcns not supplied for $(LOCAL_NAME).
Please add to your PATH if installed."
+
+ jellyfish_missing:
+- @echo "!!!!!!! WARNING jellyfish not supplied for $(LOCAL_NAME).
Please add to your PATH if installed."
++ @echo "!!!!!!! WARNING jellyfish2 not supplied for $(LOCAL_NAME).
Please add to your PATH if installed."
diff --git a/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild
b/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild
index 3c22d9b94..ce6d289c4 100644
--- a/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild
+++ b/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -23,13 +23,13 @@ DEPEND="
!x11-terms/terminator"
RDEPEND="${DEPEND}
app-shells/tcsh
- dev-perl/Log-Log4perl"
+ dev-perl/Log-Log4perl
+ sci-biology/jellyfish:2"
S="${WORKDIR}/wgs-${MY_PV}"
src_prepare() {
- # epatch \
- # "${FILESDIR}"/${P}-build.patch
+ epatch "${FILESDIR}"/${P}-rename-jellyfish.patch
tc-export CC CXX
}
@@ -69,6 +69,6 @@ src_install() {
use static-libs && dolib.a ${MY_S}/lib/*
dodoc README
- # avoid file collision
- rm -f "${D}"/usr/bin/jellyfish || die
+ # drop bundled jellyfish-2.0.0
+ rm "${ED}"/usr/bin/jellyfish || die
}
