diff options
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch | 108 | ||||
| -rw-r--r-- | sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild | 22 |
2 files changed, 76 insertions, 54 deletions
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 index f7fb44743968..238541b512f2 100644 --- a/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch +++ b/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch @@ -1,33 +1,6 @@ - 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 +@@ -254,13 +254,13 @@ # -*- makefile -*- # Linux, optimized CC := $CC @@ -46,7 +19,7 @@ index 2f0d5ea..9daf89f 100755 CXXLIBS := -pthread -ldl ARFLAGS := ruvs INSTALL/ := $target/ -@@ -272,13 +272,13 @@ EOF +@@ -272,13 +272,13 @@ # -*- makefile -*- # Linux64, optimized CC := $CC @@ -65,11 +38,37 @@ index 2f0d5ea..9daf89f 100755 CXXLIBS := -pthread -ldl ARFLAGS := ruvs INSTALL/ := $target/ -diff --git a/src/c_make.as b/src/c_make.as -index 0172807..4304589 100644 +@@ -401,8 +401,8 @@ + .O := .o + CLD := \${CC} + CXXLD := \${CXX} +-CCDEP := gcc -MM -MG +-CXXDEP := g++ -MM -MG ++CCDEP := \$(CC) -MM -MG ++CXXDEP := \$(CXX) -MM -MG + CLIBS += -lm -lbz2 + CXXLIBS += -lm -lbz2 + PYTHON := $PYTHON +--- a/kmer/Make.rules ++++ b/kmer/Make.rules +@@ -139,12 +139,12 @@ + ## EXE targets + ALL_C_EXES :=$(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 --- a/src/c_make.as +++ b/src/c_make.as -@@ -64,27 +64,27 @@ include $(LOCAL_WORK)/src/c_make.gen +@@ -64,27 +64,27 @@ ifeq ($(OSTYPE), Linux) ifeq ($(MACHINETYPE), i686) @@ -107,7 +106,7 @@ index 0172807..4304589 100644 endif endif -@@ -94,19 +94,19 @@ endif +@@ -94,19 +94,19 @@ ifeq ($(OSTYPE), FreeBSD) ifeq ($(MACHINETYPE), i386) @@ -134,7 +133,16 @@ index 0172807..4304589 100644 else ifeq ($(BUILDDEBUG), 1) ARCH_CFLAGS += -g -@@ -140,14 +140,14 @@ ifeq ($(OSTYPE), Darwin) +@@ -126,8 +126,6 @@ + + + ifeq ($(OSTYPE), Darwin) +- CC = gcc +- CXX = g++ + ARCH_CFLAGS = -D_THREAD_SAFE + + ifeq ($(MACHINETYPE), ppc) +@@ -140,14 +138,14 @@ ifeq ($(MACHINETYPE), i386) ifeq ($(BUILDDEBUG), 1) @@ -153,7 +161,7 @@ index 0172807..4304589 100644 endif endif -@@ -161,23 +161,23 @@ endif +@@ -161,23 +159,23 @@ ifeq ($(OSTYPE), SunOS) ifeq ($(MACHINETYPE), i86pc) ARCH_CFLAGS = -DBYTE_ORDER=LITTLE_ENDIAN -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads @@ -182,7 +190,7 @@ index 0172807..4304589 100644 endif endif -@@ -186,14 +186,14 @@ endif +@@ -186,14 +184,14 @@ ifeq ($(BUILDPROFILE), 1) ARCH_CFLAGS += -pg @@ -199,7 +207,7 @@ index 0172807..4304589 100644 LDFLAGS += $(ARCH_LDFLAGS) INC_IMPORT_DIRS += $(LOCAL_WORK)/src $(patsubst %, $(LOCAL_WORK)/src/%, $(strip $(SUBDIRS))) -@@ -205,7 +205,7 @@ LIB_IMPORT_DIRS += $(ARCH_LIB) +@@ -205,7 +203,7 @@ OBJ_SEARCH_PATH = $(LOCAL_OBJ) ifeq ($(SITE_NAME), JCVI) @@ -208,11 +216,31 @@ index 0172807..4304589 100644 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 @@ $(LIBRARIES): +@@ -248,10 +248,6 @@ + #### Do not redefine if (a) passed in on command line, or (b) + #### defined in an environment variable. + +-ifneq "$(origin CC)" "environment" +-CC=gcc +-endif +- + ifneq "$(origin CPPFLAGS)" "environment" + CPPFLAGS= + endif +@@ -264,10 +260,6 @@ + CDEFS= + endif + +-ifneq "$(origin CXX)" "environment" +-CXX=g++ +-endif +- + ifneq "$(origin CXXFLAGS)" "environment" + CXXFLAGS= + endif +@@ -396,12 +388,12 @@ $(C_PROGS): @ echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++"; cd $(LOCAL_OBJ); \ diff --git a/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild index fc5869667f02..a9193dfe1807 100644 --- a/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild +++ b/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 -inherit eutils toolchain-funcs +inherit toolchain-funcs DESCRIPTION="The Celera de novo whole-genome shotgun DNA sequence assembler, aka CABOG" HOMEPAGE="https://sourceforge.net/projects/wgs-assembler/" @@ -12,7 +12,6 @@ SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2" LICENSE="GPL-2" SLOT="0" KEYWORDS="amd64 x86" -IUSE="static-libs" DEPEND=" net-libs/libtirpc @@ -29,13 +28,10 @@ PATCHES=( "${FILESDIR}"/${P}-libtirpc.patch ) -src_prepare() { - default - tc-export CC CXX -} - src_configure() { - cd "${S}/kmer" + tc-export AR CC CXX + + cd kmer || die ./configure.sh || die } @@ -57,16 +53,14 @@ src_install() { 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/${MY_S}/include/* + doins -r kmer/${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 } |