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

18 files changed, 257 insertions, 49 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
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-2.1.3.ebuild b/sci-biology/jellyfish/jellyfish-2.1.3-r1.ebuild
index fd71046ac..115848f30 100644
--- a/sci-biology/jellyfish/jellyfish-2.1.3.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-2.1.4.ebuild b/sci-biology/jellyfish/jellyfish-2.1.4-r1.ebuild
index fd71046ac..248e2cef4 100644
--- a/sci-biology/jellyfish/jellyfish-2.1.4.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
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/Manifest b/sci-biology/kraken/Manifest
index c3aed1482..d27cdc56a 100644
--- a/sci-biology/kraken/Manifest
+++ b/sci-biology/kraken/Manifest
@@ -1,2 +1,2 @@
-DIST kraken-1.0.tar.gz 407131 SHA256 cec40d3545199d48388269fc1b7fda9f48ae3aa73f99ed4410e1474abe421e6a SHA512 3916890132e5573e72b0b4101ed5cb5e4c99bf9e5c799635002c6c4b23c266ea390fbd641916661ffc31f4e673c0a9d762be01c5094ba9b2241891b3aa5f49f6 WHIRLPOOL abe02b73f808320f15dfd6c8b5bf8db53788c36ecf004fae70b9d269794d28673b7da5466b77d1886f4661566a88bc3011b1f9569f599bef16afd477fb4b8668
-DIST kraken-1.0_MANUAL.html 46202 SHA256 676c374202475218e33150be0fa45112e962925192d115c31f5d126df34db38e SHA512 cfd0ac55ad662b8568683ee0fe96ed6c57a6c34b0804f120b2189e25408a9ae4e0740f58ab9314ad4a6677fb3808ad54a8a3bd410df7761b6e94529df1ee697b WHIRLPOOL a9033fc1c63a6bc236d0331ae105d6cc332fbe5ba30b3b74a74cc769e1c1cb6b62b787d50e9d6e1153dbf2de66fe333b3d3a35270f14a2916f0279cc31ccef39
+DIST kraken-1.0.tar.gz 407131 BLAKE2B 948d64b14432f0d7327fa98a0f3a647b8a5e08d4979c6636d6a9924a83adcb5e3c96925815db41513ebbb7d398920e23ae059f2ee33725e2edece77edb1477d5 SHA512 3916890132e5573e72b0b4101ed5cb5e4c99bf9e5c799635002c6c4b23c266ea390fbd641916661ffc31f4e673c0a9d762be01c5094ba9b2241891b3aa5f49f6
+DIST kraken-1.0_MANUAL.html 46202 BLAKE2B 8dc02ba8eb1ee156ce0476511f34b152e4bbc73e970806e03c69bcf896b6027f75b9c4ff7d6e4df5fc517c8f53c135f78e8094a3c3c36dc98554b47ffa3f2bea SHA512 cfd0ac55ad662b8568683ee0fe96ed6c57a6c34b0804f120b2189e25408a9ae4e0740f58ab9314ad4a6677fb3808ad54a8a3bd410df7761b6e94529df1ee697b
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
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
 }