Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 493443) +++ head/biology/Makefile (revision 493444) @@ -1,157 +1,158 @@ # $FreeBSD$ # COMMENT = Biology 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/p5-Bio-Cluster/Makefile =================================================================== --- head/biology/p5-Bio-Cluster/Makefile (nonexistent) +++ head/biology/p5-Bio-Cluster/Makefile (revision 493444) @@ -0,0 +1,27 @@ +# Created by: Po-Chuan Hsieh +# $FreeBSD$ + +PORTNAME= Bio-Cluster +PORTVERSION= 1.7.3 +CATEGORIES= biology perl5 +MASTER_SITES= CPAN +PKGNAMEPREFIX= p5- + +MAINTAINER= sunpoet@FreeBSD.org +COMMENT= BioPerl cluster modules + +LICENSE= ART10 GPLv1+ +LICENSE_COMB= dual +LICENSE_FILE= ${WRKSRC}/LICENSE + +#TODO: Add Bio::Variation::SNP +BUILD_DEPENDS= ${RUN_DEPENDS} +RUN_DEPENDS= p5-BioPerl>=0:biology/p5-BioPerl \ + p5-XML-SAX>=0:textproc/p5-XML-SAX + +USES= perl5 +USE_PERL5= configure + +NO_ARCH= yes + +.include Property changes on: head/biology/p5-Bio-Cluster/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/p5-Bio-Cluster/distinfo =================================================================== --- head/biology/p5-Bio-Cluster/distinfo (nonexistent) +++ head/biology/p5-Bio-Cluster/distinfo (revision 493444) @@ -0,0 +1,3 @@ +TIMESTAMP = 1549712664 +SHA256 (Bio-Cluster-1.7.3.tar.gz) = 1967fb3899b92f245b5bf6cb64ef076fc3f8427b1a96ca5f7b74d220b6191fbb +SIZE (Bio-Cluster-1.7.3.tar.gz) = 58304 Property changes on: head/biology/p5-Bio-Cluster/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/p5-Bio-Cluster/pkg-descr =================================================================== --- head/biology/p5-Bio-Cluster/pkg-descr (nonexistent) +++ head/biology/p5-Bio-Cluster/pkg-descr (revision 493444) @@ -0,0 +1,4 @@ +Bio::Cluster is the BioPerl cluster modules. Classes and modules here describe +the basic structure for a cluster of BioPerl objects. + +WWW: https://metacpan.org/release/Bio-Cluster Property changes on: head/biology/p5-Bio-Cluster/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/p5-Bio-Cluster/pkg-plist =================================================================== --- head/biology/p5-Bio-Cluster/pkg-plist (nonexistent) +++ head/biology/p5-Bio-Cluster/pkg-plist (revision 493444) @@ -0,0 +1,20 @@ +%%SITE_PERL%%/Bio/Cluster.pm +%%SITE_PERL%%/Bio/Cluster/ClusterFactory.pm +%%SITE_PERL%%/Bio/Cluster/FamilyI.pm +%%SITE_PERL%%/Bio/Cluster/SequenceFamily.pm +%%SITE_PERL%%/Bio/Cluster/UniGene.pm +%%SITE_PERL%%/Bio/Cluster/UniGeneI.pm +%%SITE_PERL%%/Bio/ClusterI.pm +%%SITE_PERL%%/Bio/ClusterIO.pm +%%SITE_PERL%%/Bio/ClusterIO/dbsnp.pm +%%SITE_PERL%%/Bio/ClusterIO/unigene.pm +%%PERL5_MAN3%%/Bio::Cluster.3.gz +%%PERL5_MAN3%%/Bio::Cluster::ClusterFactory.3.gz +%%PERL5_MAN3%%/Bio::Cluster::FamilyI.3.gz +%%PERL5_MAN3%%/Bio::Cluster::SequenceFamily.3.gz +%%PERL5_MAN3%%/Bio::Cluster::UniGene.3.gz +%%PERL5_MAN3%%/Bio::Cluster::UniGeneI.3.gz +%%PERL5_MAN3%%/Bio::ClusterI.3.gz +%%PERL5_MAN3%%/Bio::ClusterIO.3.gz +%%PERL5_MAN3%%/Bio::ClusterIO::dbsnp.3.gz +%%PERL5_MAN3%%/Bio::ClusterIO::unigene.3.gz Property changes on: head/biology/p5-Bio-Cluster/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