diff --git a/biology/Makefile b/biology/Makefile index 60ab10072e29..13f0cd294ee5 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,206 +1,207 @@ COMMENT = Biology SUBDIR += abyss SUBDIR += ad2vcf SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bbmap SUBDIR += bcftools SUBDIR += bedtools SUBDIR += bioawk SUBDIR += biococoa SUBDIR += biolibc SUBDIR += bioparser SUBDIR += biosoup SUBDIR += biostar-tools SUBDIR += bolt-lmm SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += checkm SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += cufflinks SUBDIR += cytoscape SUBDIR += ddocent SUBDIR += diamond SUBDIR += dsr-pdb SUBDIR += edlib SUBDIR += emboss SUBDIR += erminej SUBDIR += exonerate SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastp SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += figtree SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk SUBDIR += gcta SUBDIR += gemma SUBDIR += generand SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += graphlan SUBDIR += groopm SUBDIR += haplohseq SUBDIR += hhsuite SUBDIR += hisat2 SUBDIR += hmmer SUBDIR += htslib SUBDIR += hyphy SUBDIR += igv SUBDIR += infernal SUBDIR += iolib SUBDIR += iqtree SUBDIR += jalview SUBDIR += jellyfish SUBDIR += kallisto SUBDIR += lamarc SUBDIR += libbigwig SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += minimap2 SUBDIR += mmseqs2 SUBDIR += molden SUBDIR += mopac SUBDIR += mothur SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit SUBDIR += ncbi-entrez-direct SUBDIR += ncbi-toolkit SUBDIR += ncbi-vdb SUBDIR += ngs-sdk SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Cluster SUBDIR += p5-Bio-Coordinate SUBDIR += p5-Bio-DB-EMBL SUBDIR += p5-Bio-DB-NCBIHelper 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-Bio-Variation SUBDIR += p5-BioPerl SUBDIR += p5-BioPerl-Run SUBDIR += p5-TrimGalore SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += pbbam SUBDIR += pbseqan SUBDIR += peak-classifier SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phyml SUBDIR += picard-tools SUBDIR += plink SUBDIR += pooler SUBDIR += primer3 SUBDIR += prodigal SUBDIR += prodigy-lig SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI SUBDIR += py-bigwig SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-crossmap SUBDIR += py-cutadapt SUBDIR += py-dnaio SUBDIR += py-ete3 SUBDIR += py-gffutils SUBDIR += py-goatools SUBDIR += py-gtfparse SUBDIR += py-hits SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-multiqc + SUBDIR += py-ont-fast5-api SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pandas-charm SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += py-resdk SUBDIR += py-scikit-bio SUBDIR += py-xenaPython SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += rampler SUBDIR += readseq SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += rubygem-bio-executables SUBDIR += rubygem-bio-old-biofetch-emulator SUBDIR += rubygem-bio-shell SUBDIR += samtools SUBDIR += scrm SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqan3 SUBDIR += seqio SUBDIR += seqkit SUBDIR += seqtk SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += snpeff SUBDIR += spoa SUBDIR += sra-tools SUBDIR += stacks SUBDIR += star SUBDIR += stringtie SUBDIR += subread SUBDIR += tRNAscan-SE SUBDIR += tabixpp SUBDIR += taxonkit SUBDIR += treekin SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ucsc-userapps SUBDIR += ugene SUBDIR += unikmer SUBDIR += vcf-split SUBDIR += vcf2hap SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += viennarna SUBDIR += vsearch SUBDIR += vt SUBDIR += wise .include diff --git a/biology/py-ont-fast5-api/Makefile b/biology/py-ont-fast5-api/Makefile new file mode 100644 index 000000000000..d998d68a0e04 --- /dev/null +++ b/biology/py-ont-fast5-api/Makefile @@ -0,0 +1,42 @@ +PORTNAME= ont-fast5-api +DISTVERSIONPREFIX= release_ +DISTVERSION= 4.0.0 +CATEGORIES= biology python +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Interface to HDF5 files in Oxford Nanopore .fast5 format + +LICENSE= MPL20 +LICENSE_FILE= ${WRKSRC}/LICENSE.md + +LIB_DEPENDS= libvbz_hdf_plugin.so:archivers/vbz-compression +RUN_DEPENDS= ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}h5py>=2.2.0:science/py-h5py@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}progressbar>0:misc/py-progressbar@${PY_FLAVOR} +TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pip>=0:devel/py-pip@${PY_FLAVOR} + +USES= python +USE_PYTHON= autoplist distutils +USE_GITHUB= yes + +GH_ACCOUNT= nanoporetech +GH_PROJECT= ont_fast5_api + +NO_ARCH= yes +NO_BUILD= yes + +post-patch: + ${RM} ${WRKSRC}/ont_fast5_api/vbz_plugin/* + +pre-configure: + @${REINPLACE_CMD} -e 's|progressbar33|progressbar|g' \ + ${WRKSRC}/setup.py \ + ${WRKSRC}/README.rst \ + ${WRKSRC}/ont_fast5_api/conversion_tools/conversion_utils.py + +do-test: + @cd ${WRKSRC} && ${PYTHON_CMD} ${PYDISTUTILS_SETUP} test + +.include diff --git a/biology/py-ont-fast5-api/distinfo b/biology/py-ont-fast5-api/distinfo new file mode 100644 index 000000000000..9156cd8912ef --- /dev/null +++ b/biology/py-ont-fast5-api/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1628770827 +SHA256 (nanoporetech-ont_fast5_api-release_4.0.0_GH0.tar.gz) = 7f9b3fa0f814ff38c30e9cb21971ec61e2b3fd52fb166a8404c21bf25679e0ab +SIZE (nanoporetech-ont_fast5_api-release_4.0.0_GH0.tar.gz) = 4081125 diff --git a/biology/py-ont-fast5-api/pkg-descr b/biology/py-ont-fast5-api/pkg-descr new file mode 100644 index 000000000000..e8482d387fa0 --- /dev/null +++ b/biology/py-ont-fast5-api/pkg-descr @@ -0,0 +1,9 @@ +The ont_fast5_api is a simple interface to HDF5 files of the Oxford +Nanopore .fast5 file format. It provides: + + o Implementation of the fast5 file schema using h5py library + o Methods to interact with and reflect the fast5 file schema + o Tools to convert between multi_read and single_read formats + o Tools to compress/decompress raw data in files + +WWW: https://pypi.python.org/pypi/ont_fast5_api