proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

7 files changed, 525 insertions, 0 deletions

diff --git a/sci-biology/wgs-assembler/Manifest b/sci-biology/wgs-assembler/Manifest
new file mode 100644
index 000000000000..8a178bca08c9
--- /dev/null
+++ b/sci-biology/wgs-assembler/Manifest
@@ -0,0 +1,3 @@
+DIST wgs-5.4.tar.bz2 1876180 SHA256 698b22bd63fa2bb4fe7f164a92c92f82474bc8fc64c37704258ebb3bdc86d7bf
+DIST wgs-6.1.tar.bz2 1900084 SHA256 e00c1b64e857ea01f7e9a9f115dd91e290a380ccda217dd6a386f57754a3cff8 SHA512 3a9cfff43967bf28f557c71b387b3ca8fd56dcdaf15fa0cd1d4b845b7b4d006e8f2692b2097d281925d59bbc41eaac1c789b6993877cffd0e233a5a9050af83c WHIRLPOOL 88e9a3f85ddee01a8a17e989248857bb6483fbde59ce211986f64d8729e82174b6fc04b2f771eb1fc131706a6adb9710c75fb90be3923db8bce6387764e3fa03
+DIST wgs-7.0.tar.bz2 1952253 SHA256 fee425cf2ec6aec6e98d580cc7e43b53eb37abd7ca14e3edc1f953d2c09b3a6c SHA512 e5ef1d4533e3dd17d13c6aca9631f5300768a258f8241f3f7f90de3785bf7a340b6896febe335682c282434c9983bc4a02fe2128a5b0e7ec415dd65e0fe400ba WHIRLPOOL a158b882e51e8ff80fa4e6bcbe4322125fce65fc64900407882a728de9465b778f59cc6d543142ca65a255295e66e89e5303774eeef7a66362c5f492ae99a92b
diff --git a/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch b/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch
new file mode 100644
index 000000000000..f7fb44743968
--- /dev/null
+++ b/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch
@@ -0,0 +1,229 @@
+ kmer/Make.rules   |  4 ++--
+ kmer/configure.sh | 20 +++++++++----------
+ src/c_make.as     | 58 +++++++++++++++++++++++++++----------------------------
+ src/c_make.gen    |  4 ++--
+ 4 files changed, 43 insertions(+), 43 deletions(-)
+
+diff --git a/kmer/Make.rules b/kmer/Make.rules
+index f904b13..5c2d477 100644
+--- a/kmer/Make.rules
++++ b/kmer/Make.rules
+@@ -139,12 +139,12 @@ ${ALL_CXX_DEPS}:%.d:%
+ ## EXE targets
+ ALL_C_EXES   :=$(strip $(foreach x,${//},${${x:.=.C_EXES}}))
+ ${ALL_C_EXES}:
+-	${-CC} ${CLD} ${CLDFLAGS} -o $@ $+ ${CLIBS}
++	${-CC} ${CLD} ${CLDFLAGS} ${LDFLAGS} -o $@ $+ ${CLIBS}
+ __SUBGOALS__+=$${${1:.=.C_EXES}}
+ 
+ ALL_CXX_EXES :=$(strip $(foreach x,${//},${${x:.=.CXX_EXES}}))
+ ${ALL_CXX_EXES}:
+-	${-CXX} ${CXXLD} ${CXXLDFLAGS} -o $@ $+ ${CXXLIBS}
++	${-CXX} ${CXXLD} ${CXXLDFLAGS} ${LDFLAGS} -o $@ $+ ${CXXLIBS}
+ __SUBGOALS__+=$${${1:.=.CXX_EXES}}
+ 
+ define .RULE-install-copy-C-CXX-EXES
+diff --git a/kmer/configure.sh b/kmer/configure.sh
+index 2f0d5ea..9daf89f 100755
+--- a/kmer/configure.sh
++++ b/kmer/configure.sh
+@@ -254,13 +254,13 @@ EOF
+ # -*- makefile -*-
+ #  Linux, optimized
+ CC                := $CC
+-SHLIB_FLAGS       := -shared
+-CFLAGS_COMPILE    := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
+-CLDFLAGS          := -L/usr/local/lib
++SHLIB_FLAGS       := -shared ${LDFLAGS}
++CFLAGS_COMPILE    := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts
++CLDFLAGS          := 
+ CLIBS             := -pthread -ldl
+ CXX               := $CXX
+-CXXFLAGS_COMPILE  := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
+-CXXLDFLAGS        := -L/usr/local/lib
++CXXFLAGS_COMPILE  := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts
++CXXLDFLAGS        := 
+ CXXLIBS           := -pthread -ldl
+ ARFLAGS           := ruvs
+ INSTALL/          := $target/
+@@ -272,13 +272,13 @@ EOF
+ # -*- makefile -*-
+ #  Linux64, optimized
+ CC                := $CC
+-SHLIB_FLAGS       := -shared
+-CFLAGS_COMPILE    := -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
+-CLDFLAGS          := -L/usr/local/lib
++SHLIB_FLAGS       := -shared ${LDFLAGS}
++CFLAGS_COMPILE    := -fPIC -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts
++CLDFLAGS          := 
+ CLIBS             := -pthread -ldl
+ CXX               := $CXX
+-CXXFLAGS_COMPILE  := -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
+-CXXLDFLAGS        := -L/usr/local/lib
++CXXFLAGS_COMPILE  := -fPIC -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts
++CXXLDFLAGS        := 
+ CXXLIBS           := -pthread -ldl
+ ARFLAGS           := ruvs
+ INSTALL/          := $target/
+diff --git a/src/c_make.as b/src/c_make.as
+index 0172807..4304589 100644
+--- a/src/c_make.as
++++ b/src/c_make.as
+@@ -64,27 +64,27 @@ include $(LOCAL_WORK)/src/c_make.gen
+ 
+ ifeq ($(OSTYPE), Linux)
+   ifeq ($(MACHINETYPE), i686)
+-    ARCH_LDFLAGS  += -pthread -lm
+-    ARCH_CFLAGS   += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX
++    LINK_LIBS  += -pthread -lm
++    ARCH_CFLAGS   += -pthread -Wall  -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX
+     ARCH_LIB       = /usr/X11R6/lib
+   endif
+   ifeq ($(MACHINETYPE), amd64)
+-    ARCH_LDFLAGS  += -pthread -lm
+-    ARCH_CFLAGS   += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX
++    LINK_LIBS  += -pthread -lm
++    ARCH_CFLAGS   += -pthread -Wall  -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX
+     ARCH_LIB       = /usr/lib64 /usr/X11R6/lib64
+   endif
+   ifeq ($(MACHINETYPE), ia64)
+-    ARCH_LDFLAGS  += -pthread -lm
+-    ARCH_CFLAGS   += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
++    LINK_LIBS  += -pthread -lm
++    ARCH_CFLAGS   += -pthread -Wall  -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
+     ARCH_LIB       = /usr/X11R6/lib
+   endif
+ 
+   ifeq ($(BUILDDEBUG), 1)
+-    ARCH_CFLAGS  += -g 
+-    ARCH_LDFLAGS +=
++    ARCH_CFLAGS  +=  
++    LINK_LIBS +=
+   else
+-    ARCH_CFLAGS  += -O2
+-    ARCH_LDFLAGS += -Wl,-O1
++    ARCH_CFLAGS  += 
++    LINK_LIBS += 
+   endif
+ endif
+ 
+@@ -94,19 +94,19 @@ endif
+ 
+ ifeq ($(OSTYPE), FreeBSD)
+   ifeq ($(MACHINETYPE), i386)
+-    ARCH_LDFLAGS    += -pthread -lthr -lm
+-    ARCH_CFLAGS      = -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare
+-    ARCH_CFLAGS      = -pthread       -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare
++    LINK_LIBS    += -pthread -lthr -lm
++    ARCH_CFLAGS      = -pthread -Wall  -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare
++    ARCH_CFLAGS      = -pthread        -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare
+   endif
+   ifeq ($(MACHINETYPE), amd64)
+-    ARCH_LDFLAGS    += -pthread -lthr -lm
+-    ARCH_CFLAGS      =  -pthread               -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat
+-    ARCH_CFLAGS      =  -pthread -Wall -Wextra -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat
++    LINK_LIBS    += -pthread -lthr -lm
++    ARCH_CFLAGS      =  -pthread                -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat
++    ARCH_CFLAGS      =  -pthread -Wall -Wextra  -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat
+   endif
+ 
+   ifeq ($(BUILDCOVERAGE), 1)
+     ARCH_CFLAGS   += -g -fprofile-arcs -ftest-coverage
+-    ARCH_LDFLAGS  += -lgcov
++    LINK_LIBS  += -lgcov
+   else
+     ifeq ($(BUILDDEBUG), 1)
+       ARCH_CFLAGS   += -g
+@@ -140,14 +140,14 @@ ifeq ($(OSTYPE), Darwin)
+ 
+   ifeq ($(MACHINETYPE), i386)
+     ifeq ($(BUILDDEBUG), 1)
+-      ARCH_CFLAGS   += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -g
+-      ARCH_LDFLAGS  += -m64 -lm
++      ARCH_CFLAGS   += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wall  -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -g
++      LINK_LIBS  += -m64 -lm
+     else
+ #  Wow, -Wshorten-64-to-32  is tough
+-      ARCH_CFLAGS   += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE       -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -fast
++      ARCH_CFLAGS   += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE        -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -fast
+ #     ARCH_CFLAGS   += -Wextra
+ #     ARCH_CFLAGS   += -pedantic  (see above about pedantic)
+-      ARCH_LDFLAGS  += -m64 -lm
++      LINK_LIBS  += -m64 -lm
+     endif
+   endif
+ 
+@@ -161,23 +161,23 @@ endif
+ ifeq ($(OSTYPE), SunOS)
+   ifeq ($(MACHINETYPE), i86pc)
+     ARCH_CFLAGS    = -DBYTE_ORDER=LITTLE_ENDIAN -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads
+-    ARCH_LDFLAGS  += -lm
++    LINK_LIBS  += -lm
+   endif
+ 
+   ifeq ($(MACHINETYPE), sparc32)
+     ARCH_CFLAGS    = -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads
+-    ARCH_LDFLAGS  += -lm -lnsl -lsocket
++    LINK_LIBS  += -lm -lnsl -lsocket
+   endif
+ 
+   ifeq ($(MACHINETYPE), sparc64)
+     ARCH_CFLAGS    = -m64 -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads
+-    ARCH_LDFLAGS  += -m64 -lm -lnsl -lsocket
++    LINK_LIBS  += -lm -lnsl -lsocket
+   endif
+ 
+   ifeq ($(BUILDDEBUG), 1)
+-    ARCH_CFLAGS   += -g
++    ARCH_CFLAGS   +=
+   else
+-    ARCH_CFLAGS   += -O
++    ARCH_CFLAGS   +=
+   endif
+ endif
+ 
+@@ -186,14 +186,14 @@ endif
+ 
+ ifeq ($(BUILDPROFILE), 1)
+   ARCH_CFLAGS  += -pg
+-  ARCH_LDFLAGS += -pg
++  LINK_LIBS += -pg
+ endif
+ 
+ # One can argue that CXXFLAGS should be separate.  For now, we only
+ # add to the flags.
+ 
+ CFLAGS          += $(ARCH_CFLAGS)
+-CXXFLAGS        += $(ARCH_CFLAGS) $(ARCH_CXXFLAGS)
++CXXFLAGS        += $(ARCH_CXXFLAGS)
+ LDFLAGS         += $(ARCH_LDFLAGS)
+ 
+ INC_IMPORT_DIRS += $(LOCAL_WORK)/src $(patsubst %, $(LOCAL_WORK)/src/%, $(strip $(SUBDIRS)))
+@@ -205,7 +205,7 @@ LIB_IMPORT_DIRS += $(ARCH_LIB)
+ OBJ_SEARCH_PATH  = $(LOCAL_OBJ)
+ 
+ ifeq ($(SITE_NAME), JCVI)
+-  LDFLAGS += -lcurl
++  LINK_LIBS += -lcurl
+ endif
+ 
+ #  The order of compilation here is very carefully chosen to be the
+diff --git a/src/c_make.gen b/src/c_make.gen
+index 7b5227c..c27b777 100644
+--- a/src/c_make.gen
++++ b/src/c_make.gen
+@@ -396,12 +396,12 @@ $(LIBRARIES):
+ $(C_PROGS):
+ 	@ echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++";
+ 	cd $(LOCAL_OBJ); \
+-	  $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LDFLAGS)
++	  $(CC) $(LDFLAGS) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LINK_LIBS)
+ 
+ $(CXX_PROGS):
+ 	@ echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++";
+ 	cd $(LOCAL_OBJ); \
+-          $(CXX) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LDFLAGS)
++          $(CXX) $(LDFLAGS) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LINK_LIBS)
+ 
+ $(SCRIPT_PROGS): %.sh:
+ 	@echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++";
diff --git a/sci-biology/wgs-assembler/metadata.xml b/sci-biology/wgs-assembler/metadata.xml
new file mode 100644
index 000000000000..8e4a74368071
--- /dev/null
+++ b/sci-biology/wgs-assembler/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <upstream>
+    <remote-id type="sourceforge">wgs-assembler</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/sci-biology/wgs-assembler/wgs-assembler-5.4.ebuild b/sci-biology/wgs-assembler/wgs-assembler-5.4.ebuild
new file mode 100644
index 000000000000..1ad4d9cf9540
--- /dev/null
+++ b/sci-biology/wgs-assembler/wgs-assembler-5.4.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+inherit eutils multilib toolchain-funcs
+
+DESCRIPTION="A de novo whole-genome shotgun DNA sequence assembler, also known as the Celera Assembler and CABOG"
+HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/"
+SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+DEPEND="x11-libs/libXt
+	!x11-terms/terminator"
+RDEPEND="${DEPEND}
+	app-shells/tcsh
+	dev-perl/Log-Log4perl"
+
+S="${WORKDIR}/wgs-${PV}"
+
+src_configure() {
+	sed -i -e "s/CC *= *gcc/CC = $(tc-getCC)/" \
+		-e "s/CXX *= *g++/CXX = $(tc-getCXX)/" \
+		"${S}"/src/c_make.as || die
+	sed -i -e "s/CC *:=.*/CC := $(tc-getCC)/" \
+		-e "s/CXX *:=.*/CXX := $(tc-getCXX)/" \
+		"${S}"/kmer/configure.sh || die
+	cd "${S}/kmer"
+	./configure.sh || die
+}
+
+src_compile() {
+	# not really an install target
+	emake -C kmer -j1 install || die
+	emake -C src -j1 SITE_NAME=LOCAL || die
+}
+
+src_install() {
+	OSTYPE=$(uname)
+	MACHTYPE=$(uname -m)
+	MACHTYPE=${MACHTYPE/x86_64/amd64}
+	MY_S="${OSTYPE}-${MACHTYPE}"
+	sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) || die
+
+	sed -i '/sub getBinDirectory ()/ a return "/usr/bin";' ${MY_S}/bin/runCA* || die
+	sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die
+	sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die
+
+	dobin kmer/${MY_S}/bin/* || die
+	insinto /usr/$(get_libdir)/${PN}
+	doins kmer/${MY_S}/lib/* || die
+	# Collisions
+	# dolib.a kmer/${MY_S}/lib/* || die
+	insinto /usr/include/${PN}
+	doins kmer/${MY_S}/include/*
+
+	insinto /usr/share/${PN}
+	doins -r ${MY_S}/bin/spec
+	insinto /usr/share/${PN}/lib
+	doins -r ${MY_S}/bin/TIGR || die
+	rm -rf ${MY_S}/bin/{TIGR,spec}
+	dobin ${MY_S}/bin/* || die
+	dolib.a ${MY_S}/lib/* || die
+	dodoc README
+}
diff --git a/sci-biology/wgs-assembler/wgs-assembler-6.1.ebuild b/sci-biology/wgs-assembler/wgs-assembler-6.1.ebuild
new file mode 100644
index 000000000000..8a9114d9ecd5
--- /dev/null
+++ b/sci-biology/wgs-assembler/wgs-assembler-6.1.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+inherit eutils multilib toolchain-funcs
+
+DESCRIPTION="A de novo whole-genome shotgun DNA sequence assembler, also known as the Celera Assembler and CABOG"
+HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/"
+SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 x86"
+
+DEPEND="x11-libs/libXt
+	!x11-terms/terminator"
+RDEPEND="${DEPEND}
+	app-shells/tcsh
+	dev-perl/Log-Log4perl"
+
+S="${WORKDIR}/wgs-${PV}"
+
+src_configure() {
+	sed -i -e "s/CC *= *gcc/CC = $(tc-getCC)/" \
+		-e "s/CXX *= *g++/CXX = $(tc-getCXX)/" \
+		"${S}"/src/c_make.as || die
+	sed -i -e "s/CC *:=.*/CC := $(tc-getCC)/" \
+		-e "s/CXX *:=.*/CXX := $(tc-getCXX)/" \
+		"${S}"/kmer/configure.sh || die
+	cd "${S}/kmer"
+	./configure.sh || die
+}
+
+src_compile() {
+	# not really an install target
+	emake -C kmer -j1 install || die
+	emake -C src -j1 SITE_NAME=LOCAL || die
+}
+
+src_install() {
+	OSTYPE=$(uname)
+	MACHTYPE=$(uname -m)
+	MACHTYPE=${MACHTYPE/x86_64/amd64}
+	MY_S="${OSTYPE}-${MACHTYPE}"
+	sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) || die
+
+	sed -i '/sub getBinDirectory ()/ a return "/usr/bin";' ${MY_S}/bin/runCA* || die
+	sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die
+	sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die
+
+	dobin kmer/${MY_S}/bin/* || die
+	insinto /usr/$(get_libdir)/${PN}
+	doins kmer/${MY_S}/lib/* || die
+	# Collisions
+	# dolib.a kmer/${MY_S}/lib/* || die
+	insinto /usr/include/${PN}
+	doins kmer/${MY_S}/include/*
+
+	insinto /usr/share/${PN}
+	doins -r ${MY_S}/bin/spec
+	insinto /usr/share/${PN}/lib
+	doins -r ${MY_S}/bin/TIGR || die
+	rm -rf ${MY_S}/bin/{TIGR,spec}
+	dobin ${MY_S}/bin/* || die
+	dolib.a ${MY_S}/lib/* || die
+	dodoc README
+}
diff --git a/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild
new file mode 100644
index 000000000000..b3ac7c30813b
--- /dev/null
+++ b/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild
@@ -0,0 +1,75 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+PYTHON_DEPEND=2
+
+inherit eutils python toolchain-funcs
+
+DESCRIPTION="A de novo whole-genome shotgun DNA sequence assembler, also known as the Celera Assembler and CABOG"
+HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/"
+SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="static-libs"
+
+DEPEND="
+	x11-libs/libXt
+	!x11-terms/terminator"
+RDEPEND="${DEPEND}
+	app-shells/tcsh
+	dev-perl/Log-Log4perl"
+
+S="${WORKDIR}/wgs-${PV}"
+
+pkg_setup() {
+	python_set_active_version 2
+	python_pkg_setup
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${P}-build.patch
+	tc-export CC CXX
+}
+
+src_configure() {
+	cd "${S}/kmer"
+	./configure.sh || die
+}
+
+src_compile() {
+	# not really an install target
+	emake -C kmer -j1 install
+	emake -C src -j1 SITE_NAME=LOCAL
+}
+
+src_install() {
+	OSTYPE=$(uname)
+	MACHTYPE=$(uname -m)
+	MACHTYPE=${MACHTYPE/x86_64/amd64}
+	MY_S="${OSTYPE}-${MACHTYPE}"
+	sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) || die
+
+	sed -i '/sub getBinDirectory ()/ a return "/usr/bin";' ${MY_S}/bin/runCA* || die
+	sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die
+	sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die
+
+	dobin kmer/${MY_S}/bin/*
+	insinto /usr/$(get_libdir)/${PN}
+	use static-libs && doins kmer/${MY_S}/lib/*
+
+	insinto /usr/include/${PN}
+	doins kmer/${MY_S}/include/*
+
+	insinto /usr/share/${PN}/lib
+	doins -r ${MY_S}/bin/TIGR
+	rm -rf ${MY_S}/bin/TIGR || die
+	dobin ${MY_S}/bin/*
+	use static-libs && dolib.a ${MY_S}/lib/*
+	dodoc README
+}
diff --git a/sci-biology/wgs-assembler/wgs-assembler-7.0.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0.ebuild
new file mode 100644
index 000000000000..e25a27c40026
--- /dev/null
+++ b/sci-biology/wgs-assembler/wgs-assembler-7.0.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+inherit eutils multilib toolchain-funcs
+
+DESCRIPTION="A de novo whole-genome shotgun DNA sequence assembler, also known as the Celera Assembler and CABOG"
+HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/"
+SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="x11-libs/libXt
+	!x11-terms/terminator"
+RDEPEND="${DEPEND}
+	app-shells/tcsh
+	dev-perl/Log-Log4perl"
+
+S="${WORKDIR}/wgs-${PV}"
+
+src_configure() {
+	sed -i -e "s/CC *= *gcc/CC = $(tc-getCC)/" \
+		-e "s/CXX *= *g++/CXX = $(tc-getCXX)/" \
+		"${S}"/src/c_make.as || die
+	sed -i -e "s/CC *:=.*/CC := $(tc-getCC)/" \
+		-e "s/CXX *:=.*/CXX := $(tc-getCXX)/" \
+		"${S}"/kmer/configure.sh || die
+	cd "${S}/kmer"
+	./configure.sh || die
+}
+
+src_compile() {
+	# not really an install target
+	emake -C kmer -j1 install || die
+	emake -C src -j1 SITE_NAME=LOCAL || die
+}
+
+src_install() {
+	OSTYPE=$(uname)
+	MACHTYPE=$(uname -m)
+	MACHTYPE=${MACHTYPE/x86_64/amd64}
+	MY_S="${OSTYPE}-${MACHTYPE}"
+	sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) || die
+
+	sed -i '/sub getBinDirectory ()/ a return "/usr/bin";' ${MY_S}/bin/runCA* || die
+	sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die
+	sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die
+
+	dobin kmer/${MY_S}/bin/* || die
+	insinto /usr/$(get_libdir)/${PN}
+	doins kmer/${MY_S}/lib/* || die
+	# Collisions
+	# dolib.a kmer/${MY_S}/lib/* || die
+	insinto /usr/include/${PN}
+	doins kmer/${MY_S}/include/*
+
+	insinto /usr/share/${PN}
+	doins -r ${MY_S}/bin/spec
+	insinto /usr/share/${PN}/lib
+	doins -r ${MY_S}/bin/TIGR || die
+	rm -rf ${MY_S}/bin/{TIGR,spec}
+	dobin ${MY_S}/bin/* || die
+	dolib.a ${MY_S}/lib/* || die
+	dodoc README
+}