svn commit: r517066 - in head/biology/canu: . files
Jason W. Bacon
jwb at FreeBSD.org
Fri Nov 8 14:03:16 UTC 2019
Author: jwb
Date: Fri Nov 8 14:03:15 2019
New Revision: 517066
URL: https://svnweb.freebsd.org/changeset/ports/517066
Log:
biology/canu: Upgrade to 1.9
Numerous bug fixes and enhancements
Reported by: portscout
Deleted:
head/biology/canu/files/patch-Makefile
Modified:
head/biology/canu/Makefile
head/biology/canu/distinfo
head/biology/canu/pkg-plist
Modified: head/biology/canu/Makefile
==============================================================================
--- head/biology/canu/Makefile Fri Nov 8 13:59:51 2019 (r517065)
+++ head/biology/canu/Makefile Fri Nov 8 14:03:15 2019 (r517066)
@@ -2,8 +2,7 @@
PORTNAME= canu
DISTVERSIONPREFIX= v
-DISTVERSION= 1.8
-PORTREVISION= 5
+DISTVERSION= 1.9
CATEGORIES= biology java perl5
MAINTAINER= jwb at FreeBSD.org
Modified: head/biology/canu/distinfo
==============================================================================
--- head/biology/canu/distinfo Fri Nov 8 13:59:51 2019 (r517065)
+++ head/biology/canu/distinfo Fri Nov 8 14:03:15 2019 (r517066)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1540317173
-SHA256 (marbl-canu-v1.8_GH0.tar.gz) = 30ecfe574166f54f79606038830f68927cf0efab33bdc3c6e43fd1448fa0b2e4
-SIZE (marbl-canu-v1.8_GH0.tar.gz) = 2465314
+TIMESTAMP = 1573142752
+SHA256 (marbl-canu-v1.9_GH0.tar.gz) = 6b086ab6086c050752166500378bc4b3b3543d4c617863e894d296171cee3385
+SIZE (marbl-canu-v1.9_GH0.tar.gz) = 3410307
Modified: head/biology/canu/pkg-plist
==============================================================================
--- head/biology/canu/pkg-plist Fri Nov 8 13:59:51 2019 (r517065)
+++ head/biology/canu/pkg-plist Fri Nov 8 14:03:15 2019 (r517066)
@@ -2,16 +2,13 @@ bin/alignGFA
bin/bogart
bin/bogus
bin/canu
+bin/canu-time
bin/canu.defaults
bin/correctOverlaps
bin/dumpBlob
bin/edalign
bin/errorEstimate
bin/falconsense
-bin/fastqAnalyze
-bin/fastqSample
-bin/fastqSimulate
-bin/fastqSimulate-sort
bin/filterCorrectionLayouts
bin/filterCorrectionOverlaps
bin/findErrors
@@ -20,7 +17,10 @@ bin/generateCorrectionLayouts
bin/loadCorrectedReads
bin/loadErates
bin/loadTrimmedReads
+bin/mergeRanges
bin/meryl
+bin/meryl-import
+bin/meryl-lookup
bin/mhapConvert
bin/mmapConvert
bin/ovStoreBucketizer
@@ -30,13 +30,13 @@ bin/ovStoreDump
bin/ovStoreIndexer
bin/ovStoreSorter
bin/ovStoreStats
+bin/overlapAlign
bin/overlapConvert
bin/overlapImport
bin/overlapInCore
bin/overlapInCorePartition
bin/overlapPair
bin/prefixEditDistance-matchLimitGenerate
-bin/readConsensus
bin/sequence
bin/splitHaplotype
bin/splitReads
@@ -45,7 +45,6 @@ bin/sqStoreCreatePartition
bin/sqStoreDumpFASTQ
bin/sqStoreDumpMetaData
bin/tgStoreCompress
-bin/tgStoreCoverageStat
bin/tgStoreDump
bin/tgStoreFilter
bin/tgStoreLoad
@@ -79,3 +78,6 @@ 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
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