Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 493841) +++ head/biology/Makefile (revision 493842) @@ -1,158 +1,159 @@ # $FreeBSD$ # COMMENT = Biology + SUBDIR += abyss SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += checkm SUBDIR += chemeq SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += clustalx SUBDIR += consed SUBDIR += cytoscape SUBDIR += ddocent SUBDIR += diamond SUBDIR += dsr-pdb SUBDIR += emboss SUBDIR += exonerate SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += figtree SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += graphlan SUBDIR += grappa SUBDIR += groopm SUBDIR += hisat2 SUBDIR += hmmer SUBDIR += htslib SUBDIR += hyphy SUBDIR += igv SUBDIR += infernal 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-cxx-toolkit SUBDIR += ncbi-toolkit SUBDIR += ngs-sdk SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Cluster 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 += pbbam SUBDIR += pbcopper SUBDIR += pbseqan SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += plinkseq SUBDIR += primer3 SUBDIR += prodigal SUBDIR += prodigy-lig SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt SUBDIR += py-fastTSNE SUBDIR += py-gffutils SUBDIR += py-gtfparse SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += pycogent SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtk SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += stacks SUBDIR += stringtie SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tabixpp SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += unanimity SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += wise .include Index: head/biology/abyss/Makefile =================================================================== --- head/biology/abyss/Makefile (nonexistent) +++ head/biology/abyss/Makefile (revision 493842) @@ -0,0 +1,35 @@ +# $FreeBSD$ + +PORTNAME= abyss +DISTVERSION= 2.1.5 +CATEGORIES= biology +MASTER_SITES= http://www.bcgsc.ca/platform/bioinfo/software/${PORTNAME}/releases/${DISTVERSION}/ + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Assembly By Short Sequences: parallel, paired-end sequence assembler + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE + +BUILD_DEPENDS= ${LOCALBASE}/include/boost/version.hpp:devel/boost-libs \ + ghc:lang/ghc \ + pandoc:textproc/hs-pandoc # pandoc is required just for one man page: abyss-sealer +LIB_DEPENDS= libffi.so:devel/libffi \ + libgmp.so:math/gmp \ + libomp.so:devel/openmp +RUN_DEPENDS= bash:shells/bash \ + gmake:devel/gmake + +USES= gmake iconv:wchar_t localbase:ldflags shebangfix sqlite +SHEBANG_FILES= bin/${PORTNAME}-* +SHEBANG_LANG= make +make_OLD_CMD= /usr/bin/make +make_CMD= ${PREFIX}/bin/gmake +GNU_CONFIGURE= yes +CONFIGURE_ARGS= --without-sparsehash # configure fails to find std::hash, reported to the ML: https://groups.google.com/forum/#!topic/trans-abyss/SZDBKR5bKxs + +OPTIONS_DEFINE= DOCS + +PORTDOCS= * + +.include Property changes on: head/biology/abyss/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/abyss/distinfo =================================================================== --- head/biology/abyss/distinfo (nonexistent) +++ head/biology/abyss/distinfo (revision 493842) @@ -0,0 +1,3 @@ +TIMESTAMP = 1551061546 +SHA256 (abyss-2.1.5.tar.gz) = 65bfc8241e6ff5adf7601ae4ae93a75e3db86d6bff5d593c75aaff7f0ef41757 +SIZE (abyss-2.1.5.tar.gz) = 1201318 Property changes on: head/biology/abyss/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ 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/abyss/files/patch-Common_Timer.h =================================================================== --- head/biology/abyss/files/patch-Common_Timer.h (nonexistent) +++ head/biology/abyss/files/patch-Common_Timer.h (revision 493842) @@ -0,0 +1,11 @@ +--- Common/Timer.h.orig 2019-02-25 02:35:12 UTC ++++ Common/Timer.h +@@ -3,6 +3,8 @@ + + #include + ++#include ++ + /** + * Time the duration between the construction and destruction of this + * timer object and log that duration. Property changes on: head/biology/abyss/files/patch-Common_Timer.h ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ 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/abyss/pkg-descr =================================================================== --- head/biology/abyss/pkg-descr (nonexistent) +++ head/biology/abyss/pkg-descr (revision 493842) @@ -0,0 +1,6 @@ +ABySS is a de novo, parallel, paired-end sequence assembler that is designed for +short reads. The single-processor version is useful for assembling genomes up to +100 Mbases in size. The parallel version is implemented using MPI and is capable +of assembling larger genomes. + +WWW: http://www.bcgsc.ca/platform/bioinfo/software/abyss Property changes on: head/biology/abyss/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ 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/abyss/pkg-plist =================================================================== --- head/biology/abyss/pkg-plist (nonexistent) +++ head/biology/abyss/pkg-plist (revision 493842) @@ -0,0 +1,60 @@ +bin/ABYSS +bin/ABYSS-P +bin/AdjList +bin/Consensus +bin/DAssembler +bin/DistanceEst +bin/DistanceEst-ssq +bin/KAligner +bin/MergeContigs +bin/MergePaths +bin/Overlap +bin/ParseAligns +bin/PathConsensus +bin/PathOverlap +bin/PopBubbles +bin/SimpleGraph +bin/abyss-align +bin/abyss-bloom +bin/abyss-bloom-dbg +bin/abyss-bloom-dist.mk +bin/abyss-bowtie +bin/abyss-bowtie2 +bin/abyss-bwa +bin/abyss-bwamem +bin/abyss-bwasw +bin/abyss-db-csv +bin/abyss-db-txt +bin/abyss-dida +bin/abyss-fac +bin/abyss-fatoagp +bin/abyss-filtergraph +bin/abyss-fixmate +bin/abyss-fixmate-ssq +bin/abyss-gapfill +bin/abyss-gc +bin/abyss-index +bin/abyss-junction +bin/abyss-kaligner +bin/abyss-layout +bin/abyss-longseqdist +bin/abyss-map +bin/abyss-map-ssq +bin/abyss-mergepairs +bin/abyss-overlap +bin/abyss-paired-dbg +bin/abyss-pe +bin/abyss-samtoafg +bin/abyss-samtobreak +bin/abyss-scaffold +bin/abyss-sealer +bin/abyss-stack-size +bin/abyss-tabtomd +bin/abyss-todot +bin/abyss-tofastq +bin/konnector +bin/logcounter +man/man1/ABYSS.1.gz +man/man1/abyss-pe.1.gz +man/man1/abyss-sealer.1.gz +man/man1/abyss-tofastq.1.gz Property changes on: head/biology/abyss/pkg-plist ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ 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