reinit the tree, so we can have metadata

4 files changed, 313 insertions, 0 deletions

diff --git a/sci-biology/wgs-assembler/Manifest b/sci-biology/wgs-assembler/Manifest
new file mode 100644
index 000000000000..3767df9eb177
--- /dev/null
+++ b/sci-biology/wgs-assembler/Manifest
@@ -0,0 +1,6 @@
+AUX wgs-assembler-7.0-build.patch 10279 SHA256 23c0a916b3af24f4c12fd2c40f5e7c1559749ddf3d29f1f06c89dd27ff0fd462 SHA512 77e432319cb279d188ab74edda822f6b4dda127f1e5f1d75febb6fe0533b66d5bfd066781f1ff5d4d0d8f832c491d31ec470653b9c36b29d8280b5786783c5b9 WHIRLPOOL c964cc3b3b9394251b2701d8cdb8373184509a4ee62faa44cad5df11d0dff90ab03224d2538c888414cadeaac09a512128262e66791d3b4146c2d072d7f21052
+DIST wgs-7.0.tar.bz2 1952253 SHA256 fee425cf2ec6aec6e98d580cc7e43b53eb37abd7ca14e3edc1f953d2c09b3a6c SHA512 e5ef1d4533e3dd17d13c6aca9631f5300768a258f8241f3f7f90de3785bf7a340b6896febe335682c282434c9983bc4a02fe2128a5b0e7ec415dd65e0fe400ba WHIRLPOOL a158b882e51e8ff80fa4e6bcbe4322125fce65fc64900407882a728de9465b778f59cc6d543142ca65a255295e66e89e5303774eeef7a66362c5f492ae99a92b
+EBUILD wgs-assembler-7.0-r1.ebuild 1597 SHA256 6473cee0ef880fe8e7daf1809b0b018d20f954c0a77f9e534ae92da575cd0f3a SHA512 d874b917c4b86cfb56681473c4c99ec38bd9a681b7e0832a0e9240f2a1c20a754be30316ca4b64f579cbd8c3bb50cad18e874664f5e51e41194e6941088bcb86 WHIRLPOOL f257b4ff26490cab0e3e233438ca1cafb1be11204c0a38f28fea7ea8638928179a3ee97e18b6f71ffcfc4be5866ab5c3c4d79a3eb6c4cfefd555203f1802329e
+MISC ChangeLog 2873 SHA256 1b44aed33035cb6bcaddfe9cf4f13bab73c82508e798f5703d8c57e2712912db SHA512 cfbe4601cce21311cd4a8343de00343506bf9168ca33042f86ef2626f6b411e0d2b9078a8fba2bc52137e8f3d0795f998a0c109d3974d0298fc0ff9095fc890b WHIRLPOOL 2b25fbf95083f85d51133edbffb4b869fec45a927fafa7e7beba3f1032909c136cdd3b9c0293cf52515ad7a7526d42bf61680be500e4d5ee7020690298428476
+MISC ChangeLog-2015 2127 SHA256 92fa1def396841cb4e895cc59a0a8351099efe39b3432ef034dae491bb4cd4ff SHA512 8dc7f0416773cf810ec1a5315045829322ba4887e2b0714965d8859cf1a847fa9fb37b7f5102aaec7b4e19f63f18df2ac50e8503aabb37287cce29f8f9ddfcd1 WHIRLPOOL 9429ff376104ae8b2e219a93fa99d6ec52b39e7994ca464dc7ae72e4d6ede9110168769b1a919591bce14d3c12864ec75da2da2415129d6aebc6effd2325680a
+MISC metadata.xml 354 SHA256 e40bc21a4b4606897765d8a7e17d05d00513d64cf8b25294587150134d5e9b7b SHA512 b46f437eb224dbc7d7cec21941565ab48055f1d7b787fae7e66b135a8abeff0ea55dc191643d1e5f6212012001d98e4b7e8a7a655c9a66c9f3124bf7e700e193 WHIRLPOOL e654a2c11f819f97f8359a0cf8e57b651c45490146287954f84aaadad81a76be7fa08122b70442111c28111b6aa29a5986b3fc802ab048c9cc9ca9f955b688ea
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 "++++++++++++++++++++ " $@ "++++++++++++++++++++++";
diff --git a/sci-biology/wgs-assembler/metadata.xml b/sci-biology/wgs-assembler/metadata.xml
new file mode 100644
index 000000000000..fa8a259ff764
--- /dev/null
+++ b/sci-biology/wgs-assembler/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <upstream>
+    <remote-id type="sourceforge">wgs-assembler</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild
new file mode 100644
index 000000000000..066654dcfb92
--- /dev/null
+++ b/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild
@@ -0,0 +1,67 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="The Celera de novo whole-genome shotgun DNA sequence assembler, aka CABOG"
+HOMEPAGE="https://sourceforge.net/projects/wgs-assembler/"
+SRC_URI="mirror://sourceforge/${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}"
+
+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
+}