* [gentoo-commits] repo/gentoo:master commit in: sci-biology/wgs-assembler/files/, sci-biology/wgs-assembler/
@ 2018-04-29 21:31 Andreas Hüttel
0 siblings, 0 replies; 2+ messages in thread
From: Andreas Hüttel @ 2018-04-29 21:31 UTC (permalink / raw
To: gentoo-commits
commit: e5fab3349b68203b78b69745bbb71734fa43c515
Author: Andreas K. Hüttel <dilfridge <AT> gentoo <DOT> org>
AuthorDate: Sun Apr 29 21:30:45 2018 +0000
Commit: Andreas Hüttel <dilfridge <AT> gentoo <DOT> org>
CommitDate: Sun Apr 29 21:31:06 2018 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e5fab334
sci-biology/wgs-assembler: Revision bump using libtirpc, bug 374815
Bug: https://bugs.gentoo.org/374815
Package-Manager: Portage-2.3.31, Repoman-2.3.9
.../files/wgs-assembler-7.0-libtirpc.patch | 16 +++++
.../wgs-assembler/wgs-assembler-7.0-r2.ebuild | 72 ++++++++++++++++++++++
2 files changed, 88 insertions(+)
diff --git a/sci-biology/wgs-assembler/files/wgs-assembler-7.0-libtirpc.patch b/sci-biology/wgs-assembler/files/wgs-assembler-7.0-libtirpc.patch
new file mode 100644
index 00000000000..7269b0b73c4
--- /dev/null
+++ b/sci-biology/wgs-assembler/files/wgs-assembler-7.0-libtirpc.patch
@@ -0,0 +1,16 @@
+diff -ruN wgs-7.0.orig/src/c_make.as wgs-7.0/src/c_make.as
+--- wgs-7.0.orig/src/c_make.as 2018-04-29 23:00:02.200181987 +0200
++++ wgs-7.0/src/c_make.as 2018-04-29 23:17:33.612700507 +0200
+@@ -196,6 +196,12 @@
+ CXXFLAGS += $(ARCH_CXXFLAGS)
+ LDFLAGS += $(ARCH_LDFLAGS)
+
++# libtirpc
++
++CFLAGS += -I/usr/include/tirpc
++CXXFLAGS += -I/usr/include/tirpc
++LINK_LIBS += -ltirpc
++
+ INC_IMPORT_DIRS += $(LOCAL_WORK)/src $(patsubst %, $(LOCAL_WORK)/src/%, $(strip $(SUBDIRS)))
+ INC_IMPORT_DIRS += $(ARCH_INC)
+
diff --git a/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild
new file mode 100644
index 00000000000..192dc48173e
--- /dev/null
+++ b/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild
@@ -0,0 +1,72 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="The Celera de novo whole-genome shotgun DNA sequence assembler, aka CABOG"
+HOMEPAGE="https://sourceforge.net/projects/wgs-assembler/"
+SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="static-libs"
+
+DEPEND="
+ net-libs/libtirpc
+ x11-libs/libXt
+ !x11-terms/terminator"
+RDEPEND="${DEPEND}
+ app-shells/tcsh
+ dev-perl/Log-Log4perl"
+
+S="${WORKDIR}/wgs-${PV}"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-build.patch
+ "${FILESDIR}"/${P}-libtirpc.patch
+)
+
+src_prepare() {
+ default
+ 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
+}
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/wgs-assembler/files/, sci-biology/wgs-assembler/
@ 2020-06-21 17:41 David Seifert
0 siblings, 0 replies; 2+ messages in thread
From: David Seifert @ 2020-06-21 17:41 UTC (permalink / raw
To: gentoo-commits
commit: a21b58f18f8571ceb3d4f2fdf5abc90a3a4b8569
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 21 17:41:01 2020 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Jun 21 17:41:01 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a21b58f1
sci-biology/wgs-assembler: [QA] Pass CC/CXX to build system
Closes: https://bugs.gentoo.org/725314
Closes: https://bugs.gentoo.org/725316
Package-Manager: Portage-2.3.101, Repoman-2.3.22
Signed-off-by: David Seifert <soap <AT> gentoo.org>
.../files/wgs-assembler-7.0-build.patch | 108 +++++++++++++--------
.../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 f7fb4474396..238541b512f 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 $(LOCAL_OBJ); \
diff --git a/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild
index fc5869667f0..a9193dfe180 100644
--- a/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild
+++ b/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
DESCRIPTION="The Celera de novo whole-genome shotgun DNA sequence assembler, aka CABOG"
HOMEPAGE="https://sourceforge.net/projects/wgs-assembler/"
@@ -12,7 +12,6 @@ SRC_URI="mirror://sourceforge/${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
}
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