svn commit: r456950 - in head/biology: . canu canu/files

Jason W. Bacon jwb at FreeBSD.org
Fri Dec 22 01:30:28 UTC 2017 

Author: jwb
Date: Fri Dec 22 01:30:26 2017
New Revision: 456950
URL: https://svnweb.freebsd.org/changeset/ports/456950

Log:
  [new port] biology/canu: Single molecule sequence assembler
  
  Approved by: jrm (mentor) or wen (mentor)
  Differential Revision:  https://reviews.freebsd.org/D13574

Added:
  head/biology/canu/
  head/biology/canu/Makefile   (contents, props changed)
  head/biology/canu/distinfo   (contents, props changed)
  head/biology/canu/files/
  head/biology/canu/files/patch-src_pipelines_canu_Execution.pm   (contents, props changed)
  head/biology/canu/pkg-descr   (contents, props changed)
  head/biology/canu/pkg-plist   (contents, props changed)
Modified:
  head/biology/Makefile

Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile	Thu Dec 21 21:44:45 2017	(r456949)
+++ head/biology/Makefile	Fri Dec 22 01:30:26 2017	(r456950)
@@ -14,6 +14,7 @@
     SUBDIR += bowtie
     SUBDIR += bowtie2
     SUBDIR += bwa
+    SUBDIR += canu
     SUBDIR += cd-hit
     SUBDIR += cdbfasta
     SUBDIR += chemeq

Added: head/biology/canu/Makefile
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/canu/Makefile	Fri Dec 22 01:30:26 2017	(r456950)
@@ -0,0 +1,65 @@
+# $FreeBSD$
+
+PORTNAME=	canu
+DISTVERSIONPREFIX=	v
+DISTVERSION=	1.6
+CATEGORIES=	biology java perl5
+
+MAINTAINER=	jwb at FreeBSD.org
+COMMENT=	Single molecule sequence assembler
+
+LICENSE=	GPLv2
+LICENSE_FILE=	${WRKSRC}/README.license.GPL
+
+LIB_DEPENDS+=	libboost_regex.so:devel/boost-libs
+RUN_DEPENDS+=	gnuplot:math/gnuplot
+
+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
+
+# Makefile compiles directly into ${DESTDIR}${PREFIX}
+MAKE_ENV+=	DESTDIR=${BUILD_WRKSRC}
+
+post-patch:
+	${REINPLACE_CMD} \
+		-e 's|-O4||g' \
+		-e 's|-funroll-loops||g' \
+		-e 's|-fexpensive-optimizations||g' \
+		-e 's|amd64|${ARCH}|g' \
+		${BUILD_WRKSRC}/Makefile
+	${REINPLACE_CMD} -e 's|\\$$bin/mhap-|${JAVAJARDIR}/mhap-|g' \
+		${BUILD_WRKSRC}/pipelines/canu/OverlapMhap.pm
+	${REINPLACE_CMD} -e 's|RealBin/lib|RealBin/../${SITE_PERL_REL}/canu|g' \
+		${BUILD_WRKSRC}/pipelines/canu.pl
+
+# Reorganize according to filesystem hierarchy standard
+post-build:
+	@${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
+
+do-install:
+	cd ${BUILD_WRKSRC}${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}
+
+.include <bsd.port.mk>

Added: head/biology/canu/distinfo
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/canu/distinfo	Fri Dec 22 01:30:26 2017	(r456950)
@@ -0,0 +1,3 @@
+TIMESTAMP = 1507077399
+SHA256 (marbl-canu-v1.6_GH0.tar.gz) = 470e0ac761d69d1fecab85da810a6474b1e2387d7124290a0e4124d660766498
+SIZE (marbl-canu-v1.6_GH0.tar.gz) = 2486338

Added: head/biology/canu/files/patch-src_pipelines_canu_Execution.pm
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/canu/files/patch-src_pipelines_canu_Execution.pm	Fri Dec 22 01:30:26 2017	(r456950)
@@ -0,0 +1,13 @@
+--- 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);
+ }
+ 

Added: head/biology/canu/pkg-descr
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/canu/pkg-descr	Fri Dec 22 01:30:26 2017	(r456950)
@@ -0,0 +1,4 @@
+Canu is a fork of the Celera Assembler designed for high-noise single-molecule
+sequencing (such as the PacBio RSII or Oxford Nanopore MinION).
+
+WWW: http://canu.readthedocs.io/

Added: head/biology/canu/pkg-plist
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/canu/pkg-plist	Fri Dec 22 01:30:26 2017	(r456950)
@@ -0,0 +1,81 @@
+bin/alignGFA
+bin/bogart
+bin/bogus
+bin/canu
+bin/correctOverlaps
+bin/createFalconSenseInputs
+bin/erateEstimate
+bin/errorEstimate
+bin/estimate-mer-threshold
+bin/existDB
+bin/falcon_sense
+bin/fastqAnalyze
+bin/fastqSample
+bin/fastqSimulate
+bin/fastqSimulate-sort
+bin/filterCorrectionOverlaps
+bin/findErrors
+bin/findErrors-Dump
+bin/gatekeeperCreate
+bin/gatekeeperDumpFASTQ
+bin/gatekeeperDumpMetaData
+bin/gatekeeperPartition
+bin/generateCorrectionLayouts
+bin/leaff
+bin/maskMers
+bin/merTrim
+bin/meryl
+bin/mhapConvert
+bin/mmapConvert
+bin/ovStoreBucketizer
+bin/ovStoreBuild
+bin/ovStoreDump
+bin/ovStoreIndexer
+bin/ovStoreSorter
+bin/ovStoreStats
+bin/overlapConvert
+bin/overlapImport
+bin/overlapInCore
+bin/overlapInCorePartition
+bin/overlapPair
+bin/positionDB
+bin/prefixEditDistance-matchLimitGenerate
+bin/readConsensus
+bin/simple
+bin/splitReads
+bin/tgStoreCompress
+bin/tgStoreCoverageStat
+bin/tgStoreDump
+bin/tgStoreFilter
+bin/tgStoreLoad
+bin/tgTigDisplay
+bin/trimReads
+bin/utgcns
+lib/libcanu.a
+lib/libleaff.a
+%%SITE_PERL%%/canu/Configure.pm
+%%SITE_PERL%%/canu/Consensus.pm
+%%SITE_PERL%%/canu/CorrectReads.pm
+%%SITE_PERL%%/canu/Defaults.pm
+%%SITE_PERL%%/canu/ErrorEstimate.pm
+%%SITE_PERL%%/canu/Execution.pm
+%%SITE_PERL%%/canu/Gatekeeper.pm
+%%SITE_PERL%%/canu/Grid.pm
+%%SITE_PERL%%/canu/Grid_Cloud.pm
+%%SITE_PERL%%/canu/Grid_DNANexus.pm
+%%SITE_PERL%%/canu/Grid_LSF.pm
+%%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/Meryl.pm
+%%SITE_PERL%%/canu/Output.pm
+%%SITE_PERL%%/canu/OverlapBasedTrimming.pm
+%%SITE_PERL%%/canu/OverlapErrorAdjustment.pm
+%%SITE_PERL%%/canu/OverlapInCore.pm
+%%SITE_PERL%%/canu/OverlapMMap.pm
+%%SITE_PERL%%/canu/OverlapMhap.pm
+%%SITE_PERL%%/canu/OverlapStore.pm
+%%SITE_PERL%%/canu/Report.pm
+%%SITE_PERL%%/canu/Unitig.pm
+%%JAVAJARDIR%%/mhap-2.1.2.jar

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