Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 456949) +++ head/biology/Makefile (revision 456950) @@ -1,121 +1,122 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += ariadne SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += blat SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa + SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += chemeq SUBDIR += clustalw SUBDIR += consed SUBDIR += crux SUBDIR += diamond SUBDIR += emboss SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += fluctuate SUBDIR += garlic SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += grappa SUBDIR += hmmer SUBDIR += htslib SUBDIR += iolib SUBDIR += iqtree SUBDIR += jalview SUBDIR += jellyfish SUBDIR += kallisto SUBDIR += lagan SUBDIR += lamarc SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += molden SUBDIR += mopac SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-toolkit SUBDIR += njplot SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Coordinate SUBDIR += p5-Bio-Das SUBDIR += p5-Bio-Das-Lite SUBDIR += p5-Bio-FeatureIO SUBDIR += p5-Bio-GFF3 SUBDIR += p5-Bio-Glite SUBDIR += p5-Bio-Graphics SUBDIR += p5-Bio-MAGETAB SUBDIR += p5-Bio-NEXUS SUBDIR += p5-Bio-Phylo SUBDIR += p5-Bio-SCF SUBDIR += p5-BioPerl SUBDIR += p5-BioPerl-Run SUBDIR += p5-TrimGalore SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += plink SUBDIR += plinkseq SUBDIR += primer3 SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt SUBDIR += py-macs2 SUBDIR += py-pysam SUBDIR += pycogent SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust SUBDIR += ssaha SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tinker SUBDIR += treepuzzle SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcftools SUBDIR += velvet SUBDIR += wise SUBDIR += xmolwt .include Index: head/biology/canu/Makefile =================================================================== --- head/biology/canu/Makefile (nonexistent) +++ head/biology/canu/Makefile (revision 456950) @@ -0,0 +1,65 @@ +# $FreeBSD$ + +PORTNAME= canu +DISTVERSIONPREFIX= v +DISTVERSION= 1.6 +CATEGORIES= biology java perl5 + +MAINTAINER= jwb@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 Property changes on: head/biology/canu/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/canu/distinfo =================================================================== --- head/biology/canu/distinfo (nonexistent) +++ head/biology/canu/distinfo (revision 456950) @@ -0,0 +1,3 @@ +TIMESTAMP = 1507077399 +SHA256 (marbl-canu-v1.6_GH0.tar.gz) = 470e0ac761d69d1fecab85da810a6474b1e2387d7124290a0e4124d660766498 +SIZE (marbl-canu-v1.6_GH0.tar.gz) = 2486338 Property changes on: head/biology/canu/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +on \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/canu/files/patch-src_pipelines_canu_Execution.pm =================================================================== --- head/biology/canu/files/patch-src_pipelines_canu_Execution.pm (nonexistent) +++ head/biology/canu/files/patch-src_pipelines_canu_Execution.pm (revision 456950) @@ -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); + } + Property changes on: head/biology/canu/files/patch-src_pipelines_canu_Execution.pm ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +on \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/canu/pkg-descr =================================================================== --- head/biology/canu/pkg-descr (nonexistent) +++ head/biology/canu/pkg-descr (revision 456950) @@ -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/ Property changes on: head/biology/canu/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +on \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/canu/pkg-plist =================================================================== --- head/biology/canu/pkg-plist (nonexistent) +++ head/biology/canu/pkg-plist (revision 456950) @@ -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 Property changes on: head/biology/canu/pkg-plist ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +on \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property