biology/canu: Upgrade to 1.7 release

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15201

biology/canu/Makefile

@@ -1,16 +1,15 @@
 # $FreeBSD$
 
-PORTNAME=	canu
+PORTNAME=		canu
 DISTVERSIONPREFIX=	v
-DISTVERSION=	1.6
-PORTREVISION=	3
-CATEGORIES=	biology java perl5
+DISTVERSION=		1.7
+CATEGORIES=		biology java perl5
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Single molecule sequence assembler
 
 LICENSE=	GPLv2
-LICENSE_FILE=	${WRKSRC}/README.license.GPL
+LICENSE_FILE=	${WRKDIR}/${PORTNAME}-${PORTVERSION}/README.license.GPL
 
 LIB_DEPENDS=	libboost_regex.so:devel/boost-libs
 RUN_DEPENDS=	gnuplot:math/gnuplot
@@ -19,14 +18,12 @@ USES=		compiler:openmp gmake perl5
 USE_JAVA=	yes
 JAVA_RUN=	yes
 JAVA_VERSION=	1.8+
-
 USE_GITHUB=	yes
 GH_ACCOUNT=	marbl
 
-BUILD_WRKSRC=	${WRKSRC}/src
-
+WRKSRC_SUBDIR=	src
 # Makefile compiles directly into ${DESTDIR}${PREFIX}
-MAKE_ENV+=	DESTDIR=${BUILD_WRKSRC}
+MAKE_ENV+=	DESTDIR=${WRKSRC}
 
 post-patch:
 	${REINPLACE_CMD} \
@@ -34,33 +31,27 @@ post-patch:
 		-e 's|-funroll-loops||g' \
 		-e 's|-fexpensive-optimizations||g' \
 		-e 's|amd64|${ARCH}|g' \
-		${BUILD_WRKSRC}/Makefile
+		${WRKSRC}/Makefile
 	${REINPLACE_CMD} -e 's|\\$$bin/mhap-|${JAVAJARDIR}/mhap-|g' \
-		${BUILD_WRKSRC}/pipelines/canu/OverlapMhap.pm
+		${WRKSRC}/pipelines/canu/OverlapMhap.pm
 	${REINPLACE_CMD} -e 's|RealBin/lib|RealBin/../${SITE_PERL_REL}/canu|g' \
-		${BUILD_WRKSRC}/pipelines/canu.pl
+		${WRKSRC}/pipelines/canu.pl
 
-# Reorganize according to filesystem hierarchy standard
+# Upstream does not want to use lib/perl5/site_perl
 post-build:
-	@${MKDIR} ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/${SITE_PERL_REL}
-	@${MV} ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/bin/lib/canu \
-		${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/${SITE_PERL_REL}
-	@${RMDIR} ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/bin/lib
-	@${MV} ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/bin/*.a \
-		${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib
-	@${MKDIR} ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/${JAVAJARDIR:S,^${PREFIX}/,,}
-	@${MV} ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/bin/*.jar \
-		${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/${JAVAJARDIR:S,^${PREFIX}/,,}
-	@${RM} ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/bin/canu.defaults
+	${MKDIR} ${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/perl5
+	${MV} ${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/site_perl \
+		${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/perl5
 
 do-install:
-	cd ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH} && ${COPYTREE_BIN} bin \
-		${STAGEDIR}${PREFIX}
+	${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} \
 		`file ${STAGEDIR}${PREFIX}/bin/* | ${GREP} ELF | cut -d : -f 1`
-	cd ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH} && ${COPYTREE_SHARE} "lib share" \
-		${STAGEDIR}${PREFIX}
+	(cd ${WRKSRC}${PREFIX}/FreeBSD-${ARCH} && \
+		${COPYTREE_SHARE} "lib share" ${STAGEDIR}${PREFIX})
 
 .include <bsd.port.mk>

biology/canu/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1507077399
-SHA256 (marbl-canu-v1.6_GH0.tar.gz) = 470e0ac761d69d1fecab85da810a6474b1e2387d7124290a0e4124d660766498
-SIZE (marbl-canu-v1.6_GH0.tar.gz) = 2486338
+TIMESTAMP = 1524325169
+SHA256 (marbl-canu-v1.7_GH0.tar.gz) = c5be54b0ad20729093413e7e722a19637d32e966dc8ecd2b579ba3e4958d378a
+SIZE (marbl-canu-v1.7_GH0.tar.gz) = 2533016

biology/canu/files/patch-pipelines_canu_Execution.pm

@@ -1,6 +1,8 @@
---- src/pipelines/canu/Execution.pm.orig	2017-08-14 19:39:19 UTC
-+++ src/pipelines/canu/Execution.pm
-@@ -302,10 +302,6 @@ sub skipStage ($$@) {
+$NetBSD$
+
+--- pipelines/canu/Execution.pm.orig	2017-04-17 19:32:38 UTC
++++ pipelines/canu/Execution.pm
+@@ -293,10 +293,6 @@ sub skipStage ($$@) {
  sub getInstallDirectory () {
      my $installDir = $FindBin::RealBin;
  

biology/canu/pkg-descr

@@ -1,4 +1,14 @@
-Canu is a fork of the Celera Assembler designed for high-noise single-molecule
-sequencing (such as the PacBio RSII or Oxford Nanopore MinION).
+Canu is a fork of the Celera Assembler, designed for high-noise single-molecule
+sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).
+
+Canu is a hierarchical assembly pipeline which runs in four steps:
+
+    Detect overlaps in high-noise sequences using MHAP
+
+    Generate corrected sequence consensus
+
+    Trim corrected sequences
+
+    Assemble trimmed corrected sequences
 
 WWW: http://canu.readthedocs.io/

biology/canu/pkg-plist

@@ -2,17 +2,22 @@ bin/alignGFA
 bin/bogart
 bin/bogus
 bin/canu
+bin/canu.defaults
 bin/correctOverlaps
 bin/createFalconSenseInputs
+bin/dumpBlob
+bin/edalign
 bin/erateEstimate
 bin/errorEstimate
 bin/estimate-mer-threshold
 bin/existDB
 bin/falcon_sense
+bin/falconsense
 bin/fastqAnalyze
 bin/fastqSample
 bin/fastqSimulate
 bin/fastqSimulate-sort
+bin/filterCorrectionLayouts
 bin/filterCorrectionOverlaps
 bin/findErrors
 bin/findErrors-Dump
@@ -22,6 +27,8 @@ bin/gatekeeperDumpMetaData
 bin/gatekeeperPartition
 bin/generateCorrectionLayouts
 bin/leaff
+bin/loadCorrectedReads
+bin/loadTrimmedReads
 bin/maskMers
 bin/merTrim
 bin/meryl
@@ -41,7 +48,10 @@ bin/overlapPair
 bin/positionDB
 bin/prefixEditDistance-matchLimitGenerate
 bin/readConsensus
+bin/sequence
 bin/simple
+bin/simple-dump
+bin/splitHaplotype
 bin/splitReads
 bin/tgStoreCompress
 bin/tgStoreCoverageStat
@@ -50,6 +60,7 @@ bin/tgStoreFilter
 bin/tgStoreLoad
 bin/tgTigDisplay
 bin/trimReads
+bin/trioCanu
 bin/utgcns
 lib/libcanu.a
 lib/libleaff.a
@@ -67,7 +78,7 @@ lib/libleaff.a
 %%SITE_PERL%%/canu/Grid_PBSTorque.pm
 %%SITE_PERL%%/canu/Grid_SGE.pm
 %%SITE_PERL%%/canu/Grid_Slurm.pm
-%%SITE_PERL%%/canu/HTML.pm
+%%SITE_PERL%%/canu/HaplotypeReads.pm
 %%SITE_PERL%%/canu/Meryl.pm
 %%SITE_PERL%%/canu/Output.pm
 %%SITE_PERL%%/canu/OverlapBasedTrimming.pm
@@ -78,4 +89,4 @@ lib/libleaff.a
 %%SITE_PERL%%/canu/OverlapStore.pm
 %%SITE_PERL%%/canu/Report.pm
 %%SITE_PERL%%/canu/Unitig.pm
-%%JAVAJARDIR%%/mhap-2.1.2.jar
+%%JAVAJARDIR%%/mhap-2.1.3.jar