canu: Upgrade to 1.8

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sat Dec 22 16:42:16 2018 -0600
Changeset:	7f67635667dc8da1fcc140703e7241f2a0805d3b

Modified Files:
	canu/Makefile
	canu/PLIST
	canu/distinfo

Log Message:
canu: Upgrade to 1.8

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=7f67635667dc8da1fcc140703e7241f2a0805d3b

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 canu/Makefile | 37 ++++++++++++++++---------------------
 canu/PLIST    | 27 ++++++++-------------------
 canu/distinfo |  8 ++++----
 3 files changed, 28 insertions(+), 44 deletions(-)

diffs:
diff --git a/canu/Makefile b/canu/Makefile
index bc20404dc7..f5ee7eda95 100644
--- a/canu/Makefile
+++ b/canu/Makefile
@@ -1,9 +1,4 @@
 # $NetBSD$
-#
-###########################################################
-#                  Generated by fbsd2pkg                  #
-#              Thu Jul 20 18:34:44 CDT 2017               #
-###########################################################
 
 DISTNAME=	canu-${PV}
 CATEGORIES=	biology java
@@ -19,35 +14,35 @@ LICENSE=	gnu-gpl-v2
 
 DEPENDS+=	gnuplot>0:../../graphics/gnuplot
 
-# Screwy Makefile compiles directly into ${DESTDIR}${PREFIX}
+# Makefile compiles directly into ${DESTDIR}${PREFIX}
 SUBST_CLASSES+=		optimize
-SUBST_STAGE.optimize=	post-patch
+SUBST_STAGE.optimize=	pre-configure
 SUBST_SED.optimize+=	-e 's|-O4|-O2|g'
 SUBST_SED.optimize+=	-e 's|-funroll-loops||g'
 SUBST_SED.optimize+=	-e 's|-fexpensive-optimizations||g'
 SUBST_FILES.optimize+=	${WRKSRC}/Makefile
 
 SUBST_CLASSES+=		jar
-SUBST_STAGE.jar=	post-patch
+SUBST_STAGE.jar=	pre-configure
 SUBST_SED.jar=		-e 's|\\$$bin/mhap-|${PREFIX}/${JAVAJARDIR}/mhap-|g'
 SUBST_FILES.jar=	${WRKSRC}/pipelines/canu/OverlapMhap.pm
 
 SUBST_CLASSES+=		perl
-SUBST_STAGE.perl=	post-patch
+SUBST_STAGE.perl=	pre-configure
 SUBST_SED.perl=		-e 's|$$FindBin::RealBin/../lib/site_perl|${PREFIX}/${SITE_PERL_REL}|g'
 SUBST_FILES.perl=	${WRKSRC}/pipelines/canu.pl
 
-REPLACE_PERL+=	bogart/*.pl \
-		pipelines/*.pl \
-		bogus/*.pl \
-		bogart-analysis/*.pl \
-		overlapBasedTrimming/*.pl \
-		overlapInCore-analysis/*.pl \
-		merTrim/*.pl \
-		erateEstimate/*.pl \
-		meryl/.pl \
-		fastq-utilities/*.pl \
-		*.pl
+REPLACE_PERL+=	bogart/*.pl
+REPLACE_PERL+=	pipelines/*.pl
+REPLACE_PERL+=	bogus/*.pl
+REPLACE_PERL+=	bogart-analysis/*.pl
+REPLACE_PERL+=	overlapBasedTrimming/*.pl
+REPLACE_PERL+=	overlapInCore-analysis/*.pl
+REPLACE_PERL+=	merTrim/*.pl
+REPLACE_PERL+=	erateEstimate/*.pl
+REPLACE_PERL+=	meryl/.pl
+REPLACE_PERL+=	fastq-utilities/*.pl
+REPLACE_PERL+=	*.pl
 
 # May work on other 64-bit processors, but untested
 ONLY_FOR_PLATFORM=	*-*-x86_64
@@ -61,7 +56,7 @@ GCC_REQD+=	4.8
 WRKSRC=		${WRKDIR}/canu-${PV}/src
 MAKE_ENV+=	DESTDIR=${WRKSRC}
 
-PV=		1.7.1
+PV=		1.8
 
 TMP_INST=		${WRKSRC}${PREFIX}/${OPSYS}-${MACHINE_ARCH:S/x86_64/amd64/}
 SITE_PERL_REL=		lib/perl5/site_perl
diff --git a/canu/PLIST b/canu/PLIST
index 438a2378f3..b3e3032b3b 100644
--- a/canu/PLIST
+++ b/canu/PLIST
@@ -5,14 +5,9 @@ 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
@@ -22,21 +17,16 @@ bin/filterCorrectionLayouts
 bin/filterCorrectionOverlaps
 bin/findErrors
 bin/findErrors-Dump
-bin/gatekeeperCreate
-bin/gatekeeperDumpFASTQ
-bin/gatekeeperDumpMetaData
-bin/gatekeeperPartition
 bin/generateCorrectionLayouts
-bin/leaff
 bin/loadCorrectedReads
+bin/loadErates
 bin/loadTrimmedReads
-bin/maskMers
-bin/merTrim
 bin/meryl
 bin/mhapConvert
 bin/mmapConvert
 bin/ovStoreBucketizer
 bin/ovStoreBuild
+bin/ovStoreConfig
 bin/ovStoreDump
 bin/ovStoreIndexer
 bin/ovStoreSorter
@@ -46,14 +36,15 @@ bin/overlapImport
 bin/overlapInCore
 bin/overlapInCorePartition
 bin/overlapPair
-bin/positionDB
 bin/prefixEditDistance-matchLimitGenerate
 bin/readConsensus
 bin/sequence
-bin/simple
-bin/simple-dump
 bin/splitHaplotype
 bin/splitReads
+bin/sqStoreCreate
+bin/sqStoreCreatePartition
+bin/sqStoreDumpFASTQ
+bin/sqStoreDumpMetaData
 bin/tgStoreCompress
 bin/tgStoreCoverageStat
 bin/tgStoreDump
@@ -61,17 +52,14 @@ bin/tgStoreFilter
 bin/tgStoreLoad
 bin/tgTigDisplay
 bin/trimReads
-bin/trioCanu
 bin/utgcns
+bin/wtdbgConvert
 lib/libcanu.a
-lib/libleaff.a
 lib/perl5/site_perl/canu/Configure.pm
 lib/perl5/site_perl/canu/Consensus.pm
 lib/perl5/site_perl/canu/CorrectReads.pm
 lib/perl5/site_perl/canu/Defaults.pm
-lib/perl5/site_perl/canu/ErrorEstimate.pm
 lib/perl5/site_perl/canu/Execution.pm
-lib/perl5/site_perl/canu/Gatekeeper.pm
 lib/perl5/site_perl/canu/Grid.pm
 lib/perl5/site_perl/canu/Grid_Cloud.pm
 lib/perl5/site_perl/canu/Grid_DNANexus.pm
@@ -89,5 +77,6 @@ lib/perl5/site_perl/canu/OverlapMMap.pm
 lib/perl5/site_perl/canu/OverlapMhap.pm
 lib/perl5/site_perl/canu/OverlapStore.pm
 lib/perl5/site_perl/canu/Report.pm
+lib/perl5/site_perl/canu/SequenceStore.pm
 lib/perl5/site_perl/canu/Unitig.pm
 share/java/classes/mhap-2.1.3.jar
diff --git a/canu/distinfo b/canu/distinfo
index e35f25e2cc..a657b45f24 100644
--- a/canu/distinfo
+++ b/canu/distinfo
@@ -1,8 +1,8 @@
 $NetBSD$
 
-SHA1 (canu-1.7.1.tar.gz) = 9f3d0d07d9cf3b5430d4321f152565cc5196cb86
-RMD160 (canu-1.7.1.tar.gz) = 14f3b48584e2ffce8de3910f348fb0b5802910e6
-SHA512 (canu-1.7.1.tar.gz) = 50b2219b284292248b001c72adf80dee2fde375bc1b84e6007842b89f0a5995b862cba1dcaf40284a8f77719da035a98b36005e2958cd4397553c0878c38910c
-Size (canu-1.7.1.tar.gz) = 2535055 bytes
+SHA1 (canu-1.8.tar.gz) = 7dd79415aa5ecb95f05109f0d8d58f7cbfc336e9
+RMD160 (canu-1.8.tar.gz) = 78d4872b4034f526037ce225c699debd910bd586
+SHA512 (canu-1.8.tar.gz) = 650bc96675f371596f8e7748d4ab2d229f0262bf84cee8fed59af43d534d76095a72e4ba0b4a5ce9f561992268c317964cda2f6c89ee514f4920e2ba47fbc86c
+Size (canu-1.8.tar.gz) = 2465314 bytes
 SHA1 (patch-pipelines_canu_Defaults.pm) = 987c1e370bc81381824f86001f70da66ea251524
 SHA1 (patch-pipelines_canu_Execution.pm) = 4c8ad9a3be08a8e5885e3ef35dca33e85c344547