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Index: head/biology/canu/Makefile
===================================================================
--- head/biology/canu/Makefile
+++ head/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 @@
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:
${REINPLACE_CMD} \
@@ -34,33 +31,27 @@
-e 's|-funroll-loops||g' \
-e 's|-fexpensive-optimizations||g' \
-e 's|amd64|${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>
Index: head/biology/canu/distinfo
===================================================================
--- head/biology/canu/distinfo
+++ head/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
Index: head/biology/canu/files/patch-pipelines_canu_Execution.pm
===================================================================
--- head/biology/canu/files/patch-pipelines_canu_Execution.pm
+++ head/biology/canu/files/patch-pipelines_canu_Execution.pm
@@ -0,0 +1,15 @@
+$NetBSD$
+
+--- pipelines/canu/Execution.pm.orig 2017-04-17 19:32:38 UTC
++++ pipelines/canu/Execution.pm
+@@ -293,10 +293,6 @@ sub skipStage ($$@) {
+ sub getInstallDirectory () {
+ my $installDir = $FindBin::RealBin;
+
+- if ($installDir =~ m!^(.*)/\w+-\w+/bin$!) {
+- $installDir = $1;
+- }
+-
+ return($installDir);
+ }
+
Index: head/biology/canu/files/patch-src_pipelines_canu_Execution.pm
===================================================================
--- head/biology/canu/files/patch-src_pipelines_canu_Execution.pm
+++ head/biology/canu/files/patch-src_pipelines_canu_Execution.pm
@@ -1,13 +0,0 @@
---- src/pipelines/canu/Execution.pm.orig 2017-08-14 19:39:19 UTC
-+++ src/pipelines/canu/Execution.pm
-@@ -302,10 +302,6 @@ sub skipStage ($$@) {
- sub getInstallDirectory () {
- my $installDir = $FindBin::RealBin;
-
-- if ($installDir =~ m!^(.*)/\w+-\w+/bin$!) {
-- $installDir = $1;
-- }
--
- return($installDir);
- }
-
Index: head/biology/canu/pkg-descr
===================================================================
--- head/biology/canu/pkg-descr
+++ head/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/
Index: head/biology/canu/pkg-plist
===================================================================
--- head/biology/canu/pkg-plist
+++ head/biology/canu/pkg-plist
@@ -2,17 +2,22 @@
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/gatekeeperPartition
bin/generateCorrectionLayouts
bin/leaff
+bin/loadCorrectedReads
+bin/loadTrimmedReads
bin/maskMers
bin/merTrim
bin/meryl
@@ -41,7 +48,10 @@
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/tgStoreLoad
bin/tgTigDisplay
bin/trimReads
+bin/trioCanu
bin/utgcns
lib/libcanu.a
lib/libleaff.a
@@ -67,7 +78,7 @@
%%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 @@
%%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

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