Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 472357) +++ head/biology/Makefile (revision 472358) @@ -1,140 +1,141 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += blat SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += chemeq SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += clustalx SUBDIR += consed SUBDIR += ddocent SUBDIR += diamond SUBDIR += emboss SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += grappa SUBDIR += hmmer SUBDIR += htslib SUBDIR += hyphy 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-toolkit SUBDIR += ngs-sdk 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 += pbbam SUBDIR += pbcopper SUBDIR += pbseqan SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += plinkseq SUBDIR += primer3 SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt SUBDIR += py-macs2 + SUBDIR += py-orange3-bioinformatics 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 += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tabixpp SUBDIR += tinker SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += unanimity SUBDIR += vcftools SUBDIR += vcflib SUBDIR += velvet SUBDIR += wise SUBDIR += xmolwt .include Index: head/biology/py-orange3-bioinformatics/Makefile =================================================================== --- head/biology/py-orange3-bioinformatics/Makefile (nonexistent) +++ head/biology/py-orange3-bioinformatics/Makefile (revision 472358) @@ -0,0 +1,26 @@ +# $FreeBSD$ + +PORTNAME= orange3-bioinformatics +DISTVERSION= 3.1.0 +CATEGORIES= biology python +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Orange add-on providing common functionality for bioinformatics + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE + +RUN_DEPENDS= orange3>0:misc/orange3 \ + ${PYTHON_PKGNAMEPREFIX}Genesis-PyAPI>0:biology/py-Genesis-PyAPI@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}requests>0:www/py-requests@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}requests-cache>0:www/py-requests-cache@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}serverfiles>0:misc/py-serverfiles@${PY_FLAVOR} + +USES= python:3.4+ +USE_GITHUB= yes +GH_ACCOUNT= biolab +USE_PYTHON= distutils autoplist +NO_ARCH= yes + +.include Property changes on: head/biology/py-orange3-bioinformatics/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/py-orange3-bioinformatics/distinfo =================================================================== --- head/biology/py-orange3-bioinformatics/distinfo (nonexistent) +++ head/biology/py-orange3-bioinformatics/distinfo (revision 472358) @@ -0,0 +1,3 @@ +TIMESTAMP = 1528854565 +SHA256 (biolab-orange3-bioinformatics-3.1.0_GH0.tar.gz) = fee8c31b1099fe076c4401951f0813a1e56bbeeae8c9a5c15e78c11cfbf29e4b +SIZE (biolab-orange3-bioinformatics-3.1.0_GH0.tar.gz) = 1969698 Property changes on: head/biology/py-orange3-bioinformatics/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/py-orange3-bioinformatics/pkg-descr =================================================================== --- head/biology/py-orange3-bioinformatics/pkg-descr (nonexistent) +++ head/biology/py-orange3-bioinformatics/pkg-descr (revision 472358) @@ -0,0 +1,11 @@ +Orange Bioinformatics extends Orange, a data mining software package, with +common functionality for bioinformatics. The provided functionality can be +accessed as a Python library or through a visual programming interface (Orange +Canvas). The latter is also suitable for non-programmers. + +Orange Bioinformatics provides access to publicly available data, like GEO data +sets, GO and KEGG. All features can be combined with powerful visualization, +network exploration and data mining techniques from the Orange data mining +framework. + +WWW: https://github.com/biolab/orange3-bioinformatics Property changes on: head/biology/py-orange3-bioinformatics/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