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biology/canu: Fix build on powerpc64 and aarch64
Should also work on powerpc and arm*, but unable to test PR: 237105 Reported by: pkubaj
This commit is contained in:
Jason W. Bacon
parent
1378000847
commit
43103da79d
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=499251
@ -12,10 +12,6 @@ COMMENT= Single molecule sequence assembler
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LICENSE= GPLv2
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LICENSE_FILE= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/README.license.GPL
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BROKEN_aarch64= fails to link: undefined reference to omp_set_num_threads
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BROKEN_armv6= fails to install: mv: rename site_perl to /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-armv6/lib/perl5/site_perl: No such file or directory
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BROKEN_armv7= fails to install: mv: rename site_perl to /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-armv7/lib/perl5/site_perl: No such file or directory
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LIB_DEPENDS= libboost_regex.so:devel/boost-libs
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RUN_DEPENDS= gnuplot:math/gnuplot
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@ -28,19 +24,28 @@ JAVA_VERSION= 1.8+
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GH_ACCOUNT= marbl
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WRKSRC_SUBDIR= src
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# Makefile compiles directly into ${DESTDIR}${PREFIX}
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MAKE_ENV+= DESTDIR=${WRKSRC}
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# Upstream Makefile compiles directly into ${DESTDIR}${PREFIX} rather than
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# using a separate install target.
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MAKE_ENV= DESTDIR=${WRKSRC} CANU_BUILD_ENV=ports
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post-patch:
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${REINPLACE_CMD} \
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.include <bsd.port.pre.mk>
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# GCC 4.2.1 (still base compiler on some 2nd tier platforms) cannot build canu
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.if ${COMPILER_TYPE} == gcc && ${COMPILER_VERSION} <= 42
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USE_GCC= yes
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.endif
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pre-configure:
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@${REINPLACE_CMD} \
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-e 's|-O4||g' \
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-e 's|-funroll-loops||g' \
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-e 's|-fexpensive-optimizations||g' \
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-e 's|amd64|${ARCH}|g' \
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${WRKSRC}/Makefile
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${REINPLACE_CMD} -e 's|\\$$bin/mhap-|${JAVAJARDIR}/mhap-|g' \
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@${REINPLACE_CMD} \
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-e 's|\\$$bin/mhap-|${JAVAJARDIR}/mhap-|g' \
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${WRKSRC}/pipelines/canu/OverlapMhap.pm
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${REINPLACE_CMD} -e 's|RealBin/lib|RealBin/../${SITE_PERL_REL}/canu|g' \
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@${REINPLACE_CMD} \
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-e 's|RealBin/lib|RealBin/../${SITE_PERL_REL}/canu|g' \
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${WRKSRC}/pipelines/canu.pl
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# Upstream does not want to use lib/perl5/site_perl
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@ -55,9 +60,9 @@ do-install:
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${COPYTREE_BIN} bin ${STAGEDIR}${PREFIX})
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# STRIP_CMD fails without this on 11.1 under poudriere
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@${CHMOD} u+w ${STAGEDIR}${PREFIX}/bin/*
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${STRIP_CMD} \
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@${STRIP_CMD} \
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`file ${STAGEDIR}${PREFIX}/bin/* | ${GREP} ELF | cut -d : -f 1`
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(cd ${WRKSRC}${PREFIX}/FreeBSD-${ARCH} && \
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${COPYTREE_SHARE} "lib share" ${STAGEDIR}${PREFIX})
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.include <bsd.port.mk>
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.include <bsd.port.post.mk>
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116
biology/canu/files/patch-Makefile
Normal file
116
biology/canu/files/patch-Makefile
Normal file
@ -0,0 +1,116 @@
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--- Makefile.orig 2018-10-22 16:47:31 UTC
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+++ Makefile
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@@ -481,68 +481,65 @@ endif
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ifeq (${OSTYPE}, FreeBSD)
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-ifeq (${MACHINETYPE}, amd64)
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- CC ?= gcc48
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- CXX ?= g++48
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- # GCC
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- CXXFLAGS += -I/usr/local/include -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
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- LDFLAGS += -L/usr/local/lib -D_GLIBCXX_PARALLEL -pthread -fopenmp -rpath /usr/local/lib/gcc48 -lm -lexecinfo
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+ ifeq (${CANU_BUILD_ENV}, ports)
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- # CLANG
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- #CXXFLAGS += -I/usr/local/include -D_GLIBCXX_PARALLEL -pthread -fPIC
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- #LDFLAGS += -L/usr/local/lib -D_GLIBCXX_PARALLEL -pthread -lm -lexecinfo -lgomp
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+ #################################################
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+ # If compiling within ports system (recommended)
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+ #################################################
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- #CXXFLAGS += -Wall -Wextra -Wformat -Wno-unused -Wno-parentheses
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- CXXFLAGS += -Wall -Wextra -Wformat -Wno-unused-function -Wno-unused-parameter -Wno-unused-variable -Wno-char-subscripts -Wno-write-strings -Wno-sign-compare -Wno-format-truncation
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+ # Use architecture as defined by ports rather than uname
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+ # ${ARCH} matches uname -p, not uname -m
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+ MACHINETYPE=${ARCH}
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- # Google Performance Tools malloc and heapchecker (HEAPCHECK=normal)
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- #CXXFLAGS +=
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- #LDFLAGS += -ltcmalloc
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+ # Take compiler and most flags from the env and make command line
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+ CXXFLAGS += -D_GLIBCXX_PARALLEL -fPIC -pthread -fopenmp
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+ LDFLAGS += -D_GLIBCXX_PARALLEL -pthread -fopenmp
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- # Google Performance Tools cpu profiler (CPUPROFILE=/path)
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- #CXXFLAGS +=
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- #LDFLAGS += -lprofiler
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+ else
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- # callgrind
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- #CXXFLAGS += -g3 -Wa,--gstabs -save-temps
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+ ######################################################
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+ # If compiling outside ports system (not recommended)
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+ ######################################################
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- ifeq ($(BUILDOPTIMIZED), 1)
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- else
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- CXXFLAGS += -g3
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- endif
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+ CC ?= gcc48
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+ CXX ?= g++48
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- ifeq ($(BUILDDEBUG), 1)
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- else
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- CXXFLAGS += -O3 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
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- endif
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-endif
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-endif
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+ # GCC
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+ CXXFLAGS += -I/usr/local/include -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
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+ LDFLAGS += -L/usr/local/lib -D_GLIBCXX_PARALLEL -pthread -fopenmp -rpath /usr/local/lib/gcc48 -lm -lexecinfo
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+ # CLANG
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+ #CXXFLAGS += -I/usr/local/include -D_GLIBCXX_PARALLEL -pthread -fPIC
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+ #LDFLAGS += -L/usr/local/lib -D_GLIBCXX_PARALLEL -pthread -lm -lexecinfo -lgomp
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-ifeq (${OSTYPE}, FreeBSD)
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-ifeq (${MACHINETYPE}, arm)
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- CC ?= gcc48
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- CXX ?= g++48
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+ #CXXFLAGS += -Wall -Wextra -Wformat -Wno-unused -Wno-parentheses
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+ CXXFLAGS += -Wall -Wextra -Wformat -Wno-unused-function -Wno-unused-parameter -Wno-unused-variable -Wno-char-subscripts -Wno-write-strings -Wno-sign-compare -Wno-format-truncation
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- CXXFLAGS += -I/usr/local/include -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
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- LDFLAGS += -L/usr/local/lib -D_GLIBCXX_PARALLEL -pthread -fopenmp -rpath /usr/local/lib/gcc48 -lm
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+ # Google Performance Tools malloc and heapchecker (HEAPCHECK=normal)
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+ #CXXFLAGS +=
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+ #LDFLAGS += -ltcmalloc
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- CXXFLAGS += -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -Wno-parentheses
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- CXXFLAGS += -funroll-loops -fomit-frame-pointer
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- LDFLAGS +=
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+ # Google Performance Tools cpu profiler (CPUPROFILE=/path)
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+ #CXXFLAGS +=
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+ #LDFLAGS += -lprofiler
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- ifeq ($(BUILDOPTIMIZED), 1)
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- else
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- CXXFLAGS += -g3
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- endif
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+ # callgrind
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+ #CXXFLAGS += -g3 -Wa,--gstabs -save-temps
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- ifeq ($(BUILDDEBUG), 1)
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- else
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- CXXFLAGS += -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
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- endif
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-endif
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-endif
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+ ifeq ($(BUILDOPTIMIZED), 1)
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+ else
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+ CXXFLAGS += -g3
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+ endif
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+
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+ ifeq ($(BUILDDEBUG), 1)
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+ else
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+ CXXFLAGS += -O3 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
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+ endif
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+
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+ endif # CANU_BUILD_ENV
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+
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+endif # FreeBSD
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ifneq (,$(findstring CYGWIN, ${OSTYPE}))
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@ -1,6 +1,6 @@
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--- pipelines/canu/Defaults.pm.orig 2018-06-19 17:20:30 UTC
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--- pipelines/canu/Defaults.pm.orig 2018-10-22 16:47:31 UTC
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+++ pipelines/canu/Defaults.pm
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@@ -812,6 +812,16 @@ sub setDefaults () {
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@@ -917,6 +917,16 @@ sub setDefaults () {
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setDefault("gridEngineArraySubmitID", undef, "Grid engine configuration, not documented");
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setDefault("gridEngineJobID", undef, "Grid engine configuration, not documented");
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@ -1,6 +1,6 @@
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--- pipelines/canu/Execution.pm.orig 2018-06-18 02:42:11 UTC
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--- pipelines/canu/Execution.pm.orig 2018-10-22 16:47:31 UTC
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+++ pipelines/canu/Execution.pm
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@@ -303,10 +303,6 @@ sub skipStage ($$@) {
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@@ -333,10 +333,6 @@ sub resetIteration ($) {
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sub getInstallDirectory () {
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my $installDir = $FindBin::RealBin;
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@ -11,7 +11,7 @@
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return($installDir);
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}
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@@ -694,8 +690,8 @@ sub submitScript ($$) {
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@@ -784,8 +780,8 @@ sub submitScript ($$) {
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@ -22,7 +22,7 @@
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my $off = 0;
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# In some grids (SGE) this is the maximum size of an array job.
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@@ -725,8 +721,42 @@ sub buildGridArray ($$$$) {
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@@ -823,8 +819,42 @@ sub buildGridArray ($$$$) {
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$off = "-F \"$off\"";
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}
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@ -67,7 +67,7 @@
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return($opt, $off);
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}
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@@ -870,7 +900,7 @@ sub buildGridJob ($$$$$$$$$) {
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@@ -973,7 +1003,7 @@ sub buildGridJob ($$$$$$$$$) {
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my $jobNameT = makeUniqueJobName($jobType, $asm);
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my ($jobName, $jobOff) = buildGridArray($jobNameT, $bgnJob, $endJob, getGlobal("gridEngineArrayName"));
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