Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 449921) +++ head/biology/Makefile (revision 449922) @@ -1,114 +1,115 @@ # $FreeBSD$ # 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 += 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 += fasttree SUBDIR += fastx-toolkit SUBDIR += fluctuate SUBDIR += garlic SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += grappa SUBDIR += hmmer SUBDIR += htslib SUBDIR += iolib SUBDIR += jalview SUBDIR += jellyfish 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-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-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/p5-Bio-FeatureIO/Makefile =================================================================== --- head/biology/p5-Bio-FeatureIO/Makefile (nonexistent) +++ head/biology/p5-Bio-FeatureIO/Makefile (revision 449922) @@ -0,0 +1,28 @@ +# Created by: Po-Chuan Hsieh +# $FreeBSD$ + +PORTNAME= Bio-FeatureIO +PORTVERSION= 1.6.905 +CATEGORIES= biology perl5 +MASTER_SITES= CPAN +PKGNAMEPREFIX= p5- + +MAINTAINER= sunpoet@FreeBSD.org +COMMENT= Handler for FeatureIO + +LICENSE= ART10 GPLv1+ +LICENSE_COMB= dual +LICENSE_FILE= ${WRKSRC}/LICENSE + +BUILD_DEPENDS= p5-BioPerl>=0:biology/p5-BioPerl \ + p5-Tree-DAG_Node>=0:devel/p5-Tree-DAG_Node \ + p5-URI>=0:net/p5-URI \ + p5-XML-DOM>=0:textproc/p5-XML-DOM \ + p5-XML-DOM-XPath>=0:textproc/p5-XML-DOM-XPath +RUN_DEPENDS:= ${BUILD_DEPENDS} + +NO_ARCH= yes +USE_PERL5= configure +USES= perl5 + +.include Property changes on: head/biology/p5-Bio-FeatureIO/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-FeatureIO/distinfo =================================================================== --- head/biology/p5-Bio-FeatureIO/distinfo (nonexistent) +++ head/biology/p5-Bio-FeatureIO/distinfo (revision 449922) @@ -0,0 +1,3 @@ +TIMESTAMP = 1505488503 +SHA256 (Bio-FeatureIO-1.6.905.tar.gz) = 322e5757b374f2fb90b8f20bdbdc75631f5cb4d122f81a4d35c3a177cf950c7a +SIZE (Bio-FeatureIO-1.6.905.tar.gz) = 54906 Property changes on: head/biology/p5-Bio-FeatureIO/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-FeatureIO/pkg-descr =================================================================== --- head/biology/p5-Bio-FeatureIO/pkg-descr (nonexistent) +++ head/biology/p5-Bio-FeatureIO/pkg-descr (revision 449922) @@ -0,0 +1,19 @@ +Bio::FeatureIO is an iterator subsystem for genomic sequence features. + +Bio::FeatureIO is a handler module for the formats in the FeatureIO set (eg, +Bio::FeatureIO::GFF). It is the officially sanctioned way of getting at the +format objects, which most people should use. + +The Bio::FeatureIO system can be thought of like biological file handles. They +are attached to filehandles with smart formatting rules (eg, GFF format, or BED +format) and can either read or write feature objects (Bio::SeqFeature objects, +or more correctly, Bio::FeatureHolderI implementing objects, of which +Bio::SeqFeature is one such object). If you want to know what to do with a +Bio::SeqFeatureI object, read Bio::SeqFeatureI. + +The idea is that you request a stream object for a particular format. All the +stream objects have a notion of an internal file that is read from or written +to. A particular FeatureIO object instance is configured for either input or +output. A specific example of a stream object is the Bio::FeatureIO::gff object. + +WWW: http://search.cpan.org/dist/Bio-FeatureIO/ Property changes on: head/biology/p5-Bio-FeatureIO/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-FeatureIO/pkg-plist =================================================================== --- head/biology/p5-Bio-FeatureIO/pkg-plist (nonexistent) +++ head/biology/p5-Bio-FeatureIO/pkg-plist (revision 449922) @@ -0,0 +1,16 @@ +%%SITE_PERL%%/Bio/FeatureIO.pm +%%SITE_PERL%%/Bio/FeatureIO/bed.pm +%%SITE_PERL%%/Bio/FeatureIO/gff.pm +%%SITE_PERL%%/Bio/FeatureIO/gtf.pm +%%SITE_PERL%%/Bio/FeatureIO/interpro.pm +%%SITE_PERL%%/Bio/FeatureIO/ptt.pm +%%SITE_PERL%%/Bio/FeatureIO/vecscreen_simple.pm +%%SITE_PERL%%/Bio/SeqFeature/Annotated.pm +%%PERL5_MAN3%%/Bio::FeatureIO.3.gz +%%PERL5_MAN3%%/Bio::FeatureIO::bed.3.gz +%%PERL5_MAN3%%/Bio::FeatureIO::gff.3.gz +%%PERL5_MAN3%%/Bio::FeatureIO::gtf.3.gz +%%PERL5_MAN3%%/Bio::FeatureIO::interpro.3.gz +%%PERL5_MAN3%%/Bio::FeatureIO::ptt.3.gz +%%PERL5_MAN3%%/Bio::FeatureIO::vecscreen_simple.3.gz +%%PERL5_MAN3%%/Bio::SeqFeature::Annotated.3.gz Property changes on: head/biology/p5-Bio-FeatureIO/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