biology/canu: Upgrade to 2.1

Numerous functional improvements for ease of use and output quality
A few bug fixes

Reported by:    portscout

4 files changed, 24 insertions, 40 deletions

diff --git a/biology/canu/Makefile b/biology/canu/Makefile
index b607369ad4c6..aa5969dbecbc 100644
--- a/biology/canu/Makefile
+++ b/biology/canu/Makefile
@@ -1,9 +1,10 @@
 # $FreeBSD$
 
 PORTNAME=		canu
-DISTVERSIONPREFIX=	v
-DISTVERSION=		2.0
+DISTVERSION=		2.1
 CATEGORIES=		biology java perl5
+# Github auto-generated tarballs lack submodules
+MASTER_SITES=		https://github.com/marbl/canu/releases/download/v2.1/
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Single molecule sequence assembler
@@ -12,17 +13,17 @@ LICENSE=	GPLv2
 LICENSE_FILE=	${WRKDIR}/${PORTNAME}-${PORTVERSION}/README.license.GPL
 
 BROKEN_powerpc64=	fails to build: utgcns/libboost/boost/smart_ptr/detail/sp_counted_impl.hpp:81:5: error: 'get_deleter' declared as a 'virtual' field
+NOT_FOR_ARCHS=		armv6 armv7 i386 powerpc
+NOT_FOR_ARCHS_REASON=	__int128 is not supported on this target
 
 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
 # Upstream Makefile compiles directly into ${DESTDIR}${PREFIX} rather than
@@ -43,24 +44,22 @@ pre-configure:
 		-e 's|-fexpensive-optimizations||g' \
 		${WRKSRC}/Makefile
 	@${REINPLACE_CMD} \
-		-e 's|RealBin/lib|RealBin/../${SITE_PERL_REL}/canu|g' \
+		-e 's|RealBin/../lib/site_perl|RealBin/../${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-${ARCH}/lib/perl5
+	@${MKDIR} ${WRKSRC}/build/lib/perl5
+	${MV} ${WRKSRC}/build/lib/site_perl ${WRKSRC}/build/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
+	(cd ${WRKSRC}/build && ${COPYTREE_BIN} bin ${STAGEDIR}${PREFIX})
+	# STRIP_CMD fails without this under poudriere
 	@${CHMOD} u+w ${STAGEDIR}${PREFIX}/bin/*
 	@${STRIP_CMD} \
 		`file ${STAGEDIR}${PREFIX}/bin/* | ${GREP} ELF | cut -d : -f 1`
-	(cd ${WRKSRC}${PREFIX}/FreeBSD-${ARCH} && \
+	(cd ${WRKSRC}/build && \
 		${COPYTREE_SHARE} "lib share" ${STAGEDIR}${PREFIX})
 
 .include <bsd.port.post.mk>
diff --git a/biology/canu/distinfo b/biology/canu/distinfo
index 90ba522f9da3..0ddec4d01a04 100644
--- a/biology/canu/distinfo
+++ b/biology/canu/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1584624503
-SHA256 (marbl-canu-v2.0_GH0.tar.gz) = e2e6e8b5ec4dd4cfba5e372f4a64b2c01fbd544d4b5867746021f10771a6f4ef
-SIZE (marbl-canu-v2.0_GH0.tar.gz) = 3443777
+TIMESTAMP = 1599584712
+SHA256 (canu-2.1.tar.gz) = 73c70d2d6326bdaf471549f2d1eb7a1bf1e0fbf45cdc4a830bd6ce9fe3f3c231
+SIZE (canu-2.1.tar.gz) = 3313120
diff --git a/biology/canu/files/patch-pipelines_canu_Execution.pm b/biology/canu/files/patch-pipelines_canu_Execution.pm
index 4b489761931c..66fd808d5f48 100644
--- a/biology/canu/files/patch-pipelines_canu_Execution.pm
+++ b/biology/canu/files/patch-pipelines_canu_Execution.pm
@@ -1,17 +1,6 @@
---- pipelines/canu/Execution.pm.orig	2018-10-22 16:47:31 UTC
+--- pipelines/canu/Execution.pm.orig	2020-09-07 19:08:24 UTC
 +++ pipelines/canu/Execution.pm
-@@ -333,10 +333,6 @@ sub resetIteration ($) {
- sub getInstallDirectory () {
-     my $installDir = $FindBin::RealBin;
- 
--    if ($installDir =~ m!^(.*)/\w+-\w+/bin$!) {
--        $installDir = $1;
--    }
--
-     return($installDir);
- }
- 
-@@ -784,8 +780,8 @@ sub submitScript ($$) {
+@@ -762,8 +762,8 @@ sub submitScript ($$) {
  
  
  
@@ -22,7 +11,7 @@
      my  $off = 0;
  
      #  In some grids (SGE)   this is the maximum size of an array job.
-@@ -823,8 +819,42 @@ sub buildGridArray ($$$$) {
+@@ -803,9 +803,43 @@ sub buildGridArray ($$$$) {
          $off = "-F \"$off\"";
      }
  
@@ -35,7 +24,7 @@
 +    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( $name =~ m/^cormhap_/i && defined getGlobal( 'slurmCormhapCoreLimit' ) )
@@ -64,10 +53,11 @@
 +	    }
 +	}
 +    }
- 
++
      return($opt, $off);
  }
-@@ -973,7 +1003,7 @@ sub buildGridJob ($$$$$$$$$) {
+ 
+@@ -951,7 +985,7 @@ sub buildGridJob ($$$$$$$$$) {
      my $jobNameT               = makeUniqueJobName($jobType, $asm);
  
      my ($jobName,  $jobOff)    = buildGridArray($jobNameT, $bgnJob, $endJob, getGlobal("gridEngineArrayName"));
diff --git a/biology/canu/pkg-plist b/biology/canu/pkg-plist
index 91f8c6ebaa28..e3d2f84d51de 100644
--- a/biology/canu/pkg-plist
+++ b/biology/canu/pkg-plist
@@ -5,6 +5,7 @@ bin/canu
 bin/canu-time
 bin/canu.defaults
 bin/correctOverlaps
+bin/draw-tig
 bin/dumpBlob
 bin/edalign
 bin/errorEstimate
@@ -13,14 +14,14 @@ bin/filterCorrectionLayouts
 bin/filterCorrectionOverlaps
 bin/findErrors
 bin/findErrors-Dump
+bin/fixErrors
 bin/generateCorrectionLayouts
+bin/layoutReads
 bin/loadCorrectedReads
 bin/loadErates
 bin/loadTrimmedReads
 bin/mergeRanges
 bin/meryl
-bin/meryl-import
-bin/meryl-lookup
 bin/mhapConvert
 bin/mmapConvert
 bin/ovStoreBucketizer
@@ -37,7 +38,6 @@ bin/overlapInCore
 bin/overlapInCorePartition
 bin/overlapPair
 bin/prefixEditDistance-matchLimitGenerate
-bin/sequence
 bin/splitHaplotype
 bin/splitReads
 bin/sqStoreCreate
@@ -45,12 +45,10 @@ bin/sqStoreDumpFASTQ
 bin/sqStoreDumpMetaData
 bin/tgStoreCompress
 bin/tgStoreDump
-bin/tgStoreFilter
 bin/tgStoreLoad
 bin/tgTigDisplay
 bin/trimReads
 bin/utgcns
-bin/wtdbgConvert
 lib/libcanu.a
 %%SITE_PERL%%/canu/Configure.pm
 %%SITE_PERL%%/canu/Consensus.pm
@@ -77,6 +75,3 @@ lib/libcanu.a
 %%SITE_PERL%%/canu/SequenceStore.pm
 %%SITE_PERL%%/canu/Unitig.pm
 %%JAVAJARDIR%%/mhap-2.1.3.jar
-share/sequence/pacbio
-share/sequence/pacbio-hifi
-share/sequence/ultra-long-nanopore