Index: head/biology/canu/Makefile
===================================================================
--- head/biology/canu/Makefile	(revision 499250)
+++ head/biology/canu/Makefile	(revision 499251)
@@ -1,63 +1,68 @@
 # $FreeBSD$
 
 PORTNAME=		canu
 DISTVERSIONPREFIX=	v
 DISTVERSION=		1.8
 PORTREVISION=		3
 CATEGORIES=		biology java perl5
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Single molecule sequence assembler
 
 LICENSE=	GPLv2
 LICENSE_FILE=	${WRKDIR}/${PORTNAME}-${PORTVERSION}/README.license.GPL
 
-BROKEN_aarch64=		fails to link: undefined reference to omp_set_num_threads
-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
-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
-
 LIB_DEPENDS=	libboost_regex.so:devel/boost-libs
 RUN_DEPENDS=	gnuplot:math/gnuplot
 
 USES=		compiler:openmp gmake perl5
 USE_JAVA=	yes
 USE_GITHUB=	yes
 
 JAVA_RUN=	yes
 JAVA_VERSION=	1.8+
 GH_ACCOUNT=	marbl
 
 WRKSRC_SUBDIR=	src
-# Makefile compiles directly into ${DESTDIR}${PREFIX}
-MAKE_ENV+=	DESTDIR=${WRKSRC}
+# Upstream Makefile compiles directly into ${DESTDIR}${PREFIX} rather than
+# using a separate install target.
+MAKE_ENV=	DESTDIR=${WRKSRC} CANU_BUILD_ENV=ports
 
-post-patch:
-	${REINPLACE_CMD} \
+.include <bsd.port.pre.mk>
+
+# GCC 4.2.1 (still base compiler on some 2nd tier platforms) cannot build canu
+.if ${COMPILER_TYPE} == gcc && ${COMPILER_VERSION} <= 42
+USE_GCC=	yes
+.endif
+
+pre-configure:
+	@${REINPLACE_CMD} \
 		-e 's|-O4||g' \
 		-e 's|-funroll-loops||g' \
 		-e 's|-fexpensive-optimizations||g' \
-		-e 's|amd64|${ARCH}|g' \
 		${WRKSRC}/Makefile
-	${REINPLACE_CMD} -e 's|\\$$bin/mhap-|${JAVAJARDIR}/mhap-|g' \
+	@${REINPLACE_CMD} \
+		-e 's|\\$$bin/mhap-|${JAVAJARDIR}/mhap-|g' \
 		${WRKSRC}/pipelines/canu/OverlapMhap.pm
-	${REINPLACE_CMD} -e 's|RealBin/lib|RealBin/../${SITE_PERL_REL}/canu|g' \
+	@${REINPLACE_CMD} \
+		-e 's|RealBin/lib|RealBin/../${SITE_PERL_REL}/canu|g' \
 		${WRKSRC}/pipelines/canu.pl
 
 # Upstream does not want to use lib/perl5/site_perl
 post-build:
 	@${MKDIR} ${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/perl5
 	${MV} ${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/site_perl \
 		${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/perl5
 
 do-install:
 	@${MKDIR} ${STAGEDIR}${PREFIX}
 	(cd ${WRKSRC}${PREFIX}/FreeBSD-${ARCH} && \
 		${COPYTREE_BIN} bin ${STAGEDIR}${PREFIX})
 	# STRIP_CMD fails without this on 11.1 under poudriere
 	@${CHMOD} u+w ${STAGEDIR}${PREFIX}/bin/*
-	${STRIP_CMD} \
+	@${STRIP_CMD} \
 		`file ${STAGEDIR}${PREFIX}/bin/* | ${GREP} ELF | cut -d : -f 1`
 	(cd ${WRKSRC}${PREFIX}/FreeBSD-${ARCH} && \
 		${COPYTREE_SHARE} "lib share" ${STAGEDIR}${PREFIX})
 
-.include <bsd.port.mk>
+.include <bsd.port.post.mk>
Index: head/biology/canu/files/patch-Makefile
===================================================================
--- head/biology/canu/files/patch-Makefile	(nonexistent)
+++ head/biology/canu/files/patch-Makefile	(revision 499251)
@@ -0,0 +1,116 @@
+--- Makefile.orig	2018-10-22 16:47:31 UTC
++++ Makefile
+@@ -481,68 +481,65 @@ endif
+ 
+ 
+ ifeq (${OSTYPE}, FreeBSD)
+-ifeq (${MACHINETYPE}, amd64)
+-  CC       ?= gcc48
+-  CXX      ?= g++48
+ 
+-  #  GCC
+-  CXXFLAGS  += -I/usr/local/include -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
+-  LDFLAGS   += -L/usr/local/lib     -D_GLIBCXX_PARALLEL -pthread -fopenmp -rpath /usr/local/lib/gcc48 -lm -lexecinfo
++  ifeq (${CANU_BUILD_ENV}, ports)
+ 
+-  #  CLANG
+-  #CXXFLAGS  += -I/usr/local/include -D_GLIBCXX_PARALLEL -pthread -fPIC
+-  #LDFLAGS   += -L/usr/local/lib     -D_GLIBCXX_PARALLEL -pthread -lm -lexecinfo -lgomp
++    #################################################
++    # If compiling within ports system (recommended)
++    #################################################
+ 
+-  #CXXFLAGS  += -Wall -Wextra -Wformat  -Wno-unused   -Wno-parentheses
+-  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
++    # Use architecture as defined by ports rather than uname
++    # ${ARCH} matches uname -p, not uname -m
++    MACHINETYPE=${ARCH}
+ 
+-  #  Google Performance Tools malloc and heapchecker (HEAPCHECK=normal)
+-  #CXXFLAGS  +=
+-  #LDFLAGS   += -ltcmalloc
++    # Take compiler and most flags from the env and make command line
++    CXXFLAGS  += -D_GLIBCXX_PARALLEL -fPIC -pthread -fopenmp
++    LDFLAGS   += -D_GLIBCXX_PARALLEL -pthread -fopenmp
+ 
+-  #  Google Performance Tools cpu profiler (CPUPROFILE=/path)
+-  #CXXFLAGS  +=
+-  #LDFLAGS   += -lprofiler
++  else
+ 
+-  #  callgrind
+-  #CXXFLAGS  += -g3 -Wa,--gstabs -save-temps
++    ######################################################
++    # If compiling outside ports system (not recommended)
++    ######################################################
+ 
+-  ifeq ($(BUILDOPTIMIZED), 1)
+-  else
+-    CXXFLAGS += -g3
+-  endif
++    CC       ?= gcc48
++    CXX      ?= g++48
+ 
+-  ifeq ($(BUILDDEBUG), 1)
+-  else
+-    CXXFLAGS += -O3 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
+-  endif
+-endif
+-endif
++    #  GCC
++    CXXFLAGS  += -I/usr/local/include -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
++    LDFLAGS   += -L/usr/local/lib     -D_GLIBCXX_PARALLEL -pthread -fopenmp -rpath /usr/local/lib/gcc48 -lm -lexecinfo
+ 
++    #  CLANG
++    #CXXFLAGS  += -I/usr/local/include -D_GLIBCXX_PARALLEL -pthread -fPIC
++    #LDFLAGS   += -L/usr/local/lib     -D_GLIBCXX_PARALLEL -pthread -lm -lexecinfo -lgomp
+ 
+-ifeq (${OSTYPE}, FreeBSD)
+-ifeq (${MACHINETYPE}, arm)
+-  CC       ?= gcc48
+-  CXX      ?= g++48
++    #CXXFLAGS  += -Wall -Wextra -Wformat  -Wno-unused   -Wno-parentheses
++    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
+ 
+-  CXXFLAGS  += -I/usr/local/include -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
+-  LDFLAGS   += -L/usr/local/lib     -D_GLIBCXX_PARALLEL -pthread -fopenmp -rpath /usr/local/lib/gcc48 -lm
++    #  Google Performance Tools malloc and heapchecker (HEAPCHECK=normal)
++    #CXXFLAGS  +=
++    #LDFLAGS   += -ltcmalloc
+ 
+-  CXXFLAGS  += -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -Wno-parentheses
+-  CXXFLAGS  += -funroll-loops -fomit-frame-pointer
+-  LDFLAGS   += 
++    #  Google Performance Tools cpu profiler (CPUPROFILE=/path)
++    #CXXFLAGS  +=
++    #LDFLAGS   += -lprofiler
+ 
+-  ifeq ($(BUILDOPTIMIZED), 1)
+-  else
+-    CXXFLAGS += -g3
+-  endif
++    #  callgrind
++    #CXXFLAGS  += -g3 -Wa,--gstabs -save-temps
+ 
+-  ifeq ($(BUILDDEBUG), 1)
+-  else
+-    CXXFLAGS += -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
+-  endif
+-endif
+-endif
++    ifeq ($(BUILDOPTIMIZED), 1)
++    else
++      CXXFLAGS += -g3
++    endif
++
++    ifeq ($(BUILDDEBUG), 1)
++    else
++      CXXFLAGS += -O3 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
++    endif
++
++  endif		# CANU_BUILD_ENV
++
++endif		# FreeBSD
+ 
+ 
+ ifneq (,$(findstring CYGWIN, ${OSTYPE}))

Property changes on: head/biology/canu/files/patch-Makefile
___________________________________________________________________
Added: fbsd:nokeywords
## -0,0 +1 ##
+yes
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Index: head/biology/canu/files/patch-pipelines_canu_Defaults.pm
===================================================================
--- head/biology/canu/files/patch-pipelines_canu_Defaults.pm	(revision 499250)
+++ head/biology/canu/files/patch-pipelines_canu_Defaults.pm	(revision 499251)
@@ -1,19 +1,19 @@
---- pipelines/canu/Defaults.pm.orig	2018-06-19 17:20:30 UTC
+--- pipelines/canu/Defaults.pm.orig	2018-10-22 16:47:31 UTC
 +++ pipelines/canu/Defaults.pm
-@@ -812,6 +812,16 @@ sub setDefaults () {
+@@ -917,6 +917,16 @@ sub setDefaults () {
      setDefault("gridEngineArraySubmitID",             undef, "Grid engine configuration, not documented");
      setDefault("gridEngineJobID",                     undef, "Grid engine configuration, not documented");
  
 +    #####  Slurm-specific parameters for controlling the number of
 +    #####  cores / tasks dispatched per step or globally (WIP)
 +
 +    setDefault( 'slurmCormhapCoreLimit', undef, 'Maximum number of cores allocated for MHAP pre-computing and alignment within the correction phase' );
 +    setDefault( 'slurmOvbCoreLimit', undef, 'Maximum number of single-core tasks dispatched for the ovlStore bucketizing step within the trimming phase' );
 +    setDefault( 'slurmOvsCoreLimit', undef, 'Maximum number of single-core tasks dispatched for the ovlStore sorting step within the trimming phase' );
 +    setDefault( 'slurmRedCoreLimit', undef, 'Maximum number of cores allocated for read error detection within the unitigging phase' );
 +    setDefault( 'slurmArrayTaskLimit', undef, 'Maximum number of tasks permitted for each step throughout assembly' );
 +    setDefault( 'slurmArrayCoreLimit', undef, 'Maximum number of cores allocated for each step throughout assembly' );
 +
      #####  Grid Engine Pipeline
  
      setDefault("useGrid", 1, "If 'true', enable grid-based execution; if 'false', run all jobs on the local machine; if 'remote', create jobs for grid execution but do not submit; default 'true'");
Index: head/biology/canu/files/patch-pipelines_canu_Execution.pm
===================================================================
--- head/biology/canu/files/patch-pipelines_canu_Execution.pm	(revision 499250)
+++ head/biology/canu/files/patch-pipelines_canu_Execution.pm	(revision 499251)
@@ -1,78 +1,78 @@
---- pipelines/canu/Execution.pm.orig	2018-06-18 02:42:11 UTC
+--- pipelines/canu/Execution.pm.orig	2018-10-22 16:47:31 UTC
 +++ pipelines/canu/Execution.pm
-@@ -303,10 +303,6 @@ sub skipStage ($$@) {
+@@ -333,10 +333,6 @@ sub resetIteration ($) {
  sub getInstallDirectory () {
      my $installDir = $FindBin::RealBin;
  
 -    if ($installDir =~ m!^(.*)/\w+-\w+/bin$!) {
 -        $installDir = $1;
 -    }
 -
      return($installDir);
  }
  
-@@ -694,8 +690,8 @@ sub submitScript ($$) {
+@@ -784,8 +780,8 @@ sub submitScript ($$) {
  
  
  
 -sub buildGridArray ($$$$) {
 -    my ($name, $bgn, $end, $opt) = @_;
 +sub buildGridArray (@) {
 +    my ( $name, $bgn, $end, $opt, $thr ) = @_;
      my  $off = 0;
  
      #  In some grids (SGE)   this is the maximum size of an array job.
-@@ -725,8 +721,42 @@ sub buildGridArray ($$$$) {
+@@ -823,8 +819,42 @@ sub buildGridArray ($$$$) {
          $off = "-F \"$off\"";
      }
  
 -    $opt =~ s/ARRAY_NAME/$name/g;        #  Replace ARRAY_NAME with 'job name'
 -    $opt =~ s/ARRAY_JOBS/$bgn-$end/g;    #  Replace ARRAY_JOBS with 'bgn-end'
 +    if( $opt =~ m/(ARRAY_NAME)/ )
 +    {
 +	$opt =~ s/$1/$name/; # Replace ARRAY_NAME with 'job name'
 +    }
 +    elsif( $opt =~ m/(ARRAY_JOBS)/ )
 +    {
 +	$opt =~ s/$1/$bgn-$end/; # Replace ARRAY_JOBS with 'bgn-end'
 +
 +	if( lc( getGlobal( 'gridEngine' ) ) eq 'slurm' && $end > 1 )
 +	{
 +	    if( $name =~ m/^cormhap_/i && defined getGlobal( 'slurmCormhapCoreLimit' ) )
 +	    {
 +		$opt .= '%' . int( getGlobal( 'slurmCormhapCoreLimit' ) / $thr );
 +	    }
 +	    elsif( $name =~ m/^ovb_/i && defined getGlobal( 'slurmOvbCoreLimit' ) )
 +	    {
 +		$opt .= '%' . getGlobal( 'slurmOvbCoreLimit' );
 +	    }
 +	    elsif( $name =~ m/^ovs_/i && defined getGlobal( 'slurmOvsCoreLimit' ) )
 +	    {
 +		$opt .= '%' . getGlobal( 'slurmOvsCoreLimit' );
 +	    }
 +	    elsif( $name =~ m/^red_/i && defined getGlobal( 'slurmRedCoreLimit' ) )
 +	    {
 +		$opt .= '%' . int( getGlobal( 'slurmRedCoreLimit' ) / $thr );
 +	    }
 +	    elsif( defined getGlobal( 'slurmArrayTaskLimit' ) )
 +	    {
 +		$opt .= '%' . getGlobal( 'slurmArrayTaskLimit' );
 +	    }
 +	    elsif( defined getGlobal( 'slurmArrayCoreLimit' ) )
 +	    {
 +		$opt .= '%' . int( getGlobal( 'slurmArrayCoreLimit' ) / $thr );
 +	    }
 +	}
 +    }
  
      return($opt, $off);
  }
-@@ -870,7 +900,7 @@ sub buildGridJob ($$$$$$$$$) {
+@@ -973,7 +1003,7 @@ sub buildGridJob ($$$$$$$$$) {
      my $jobNameT               = makeUniqueJobName($jobType, $asm);
  
      my ($jobName,  $jobOff)    = buildGridArray($jobNameT, $bgnJob, $endJob, getGlobal("gridEngineArrayName"));
 -    my ($arrayOpt, $arrayOff)  = buildGridArray($jobNameT, $bgnJob, $endJob, getGlobal("gridEngineArrayOption"));
 +    my ( $arrayOpt, $arrayOff ) = buildGridArray( $jobNameT, $bgnJob, $endJob, getGlobal( "gridEngineArrayOption" ), $thr );
  
      my $outputOption           = buildOutputOption($path, $script);