diff --git a/biology/Makefile b/biology/Makefile index 9f2f693fcfc5..eafb7136ce09 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,260 +1,261 @@ COMMENT = Biology SUBDIR += R-cran-Biobase SUBDIR += R-cran-BiocGenerics SUBDIR += R-cran-BiocManager SUBDIR += abyss SUBDIR += ad2vcf SUBDIR += andi SUBDIR += artemis SUBDIR += atac-seq SUBDIR += augustus SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bamutil SUBDIR += barrnap SUBDIR += bbmap SUBDIR += bcf-score SUBDIR += bcftools SUBDIR += bedtools SUBDIR += bfc SUBDIR += bifrost SUBDIR += bio-mocha SUBDIR += bioawk SUBDIR += biococoa SUBDIR += biolibc SUBDIR += biolibc-tools SUBDIR += bioparser SUBDIR += biosig SUBDIR += biosoup SUBDIR += biostar-tools SUBDIR += bolt-lmm SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += btllib SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += chip-seq SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += coverm SUBDIR += cufflinks SUBDIR += cytoscape SUBDIR += ddocent SUBDIR += diamond SUBDIR += dsr-pdb SUBDIR += edlib SUBDIR += emboss SUBDIR += erminej SUBDIR += exonerate SUBDIR += fasda SUBDIR += fasda-utils SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastani SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastp SUBDIR += fastq-trim SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += fermi-lite SUBDIR += figtree SUBDIR += flash SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk SUBDIR += gcta SUBDIR += gemma SUBDIR += generand SUBDIR += gff2ps SUBDIR += gffread SUBDIR += gkl 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 += kmcp SUBDIR += lamarc SUBDIR += libbigwig SUBDIR += libcombine SUBDIR += libgff SUBDIR += libgtextutils SUBDIR += libneurosim SUBDIR += libnuml SUBDIR += libsbml SUBDIR += libsedml SUBDIR += linux-foldingathome SUBDIR += locarna SUBDIR += mafft SUBDIR += mapm3 SUBDIR += mashmap SUBDIR += mca-calling SUBDIR += megahit SUBDIR += metaeuk SUBDIR += migrate SUBDIR += minimap2 SUBDIR += mmseqs2 SUBDIR += molden SUBDIR += mothur SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit SUBDIR += ncbi-entrez-direct 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-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 += peak-classifier SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phyml SUBDIR += picard-tools SUBDIR += plink SUBDIR += pooler SUBDIR += preseq SUBDIR += primer3 SUBDIR += prodigal SUBDIR += prodigy-lig SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI SUBDIR += py-PySCeS SUBDIR += py-bcbio-gff SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-biosig SUBDIR += py-bx-python SUBDIR += py-crossmap SUBDIR += py-cutadapt SUBDIR += py-deeptools SUBDIR += py-deeptoolsintervals SUBDIR += py-dna-features-viewer SUBDIR += py-dnaio SUBDIR += py-ete3 SUBDIR += py-gffutils SUBDIR += py-goatools SUBDIR += py-gtfparse SUBDIR += py-hits SUBDIR += py-htseq SUBDIR += py-libnuml SUBDIR += py-libsedml SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-macs3 SUBDIR += py-mrcfile SUBDIR += py-multiqc SUBDIR += py-newick SUBDIR += py-ont-fast5-api SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pandas-charm SUBDIR += py-py2bit SUBDIR += py-pybigwig SUBDIR += py-pyfaidx + SUBDIR += py-pydeseq2 SUBDIR += py-pyrodigal SUBDIR += py-pysam SUBDIR += py-python-libsbml SUBDIR += py-pywgsim SUBDIR += py-resdk SUBDIR += py-scikit-bio SUBDIR += py-valerius SUBDIR += py-xenaPython SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += rampler SUBDIR += readseq SUBDIR += rna-seq SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += rubygem-bio-executables SUBDIR += rubygem-bio-old-biofetch-emulator SUBDIR += rubygem-bio-shell SUBDIR += salmon SUBDIR += sam2pairwise SUBDIR += samtools SUBDIR += scrm SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqan3 SUBDIR += seqkit SUBDIR += seqtk SUBDIR += seqwish SUBDIR += sigviewer 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 += wfa2-lib SUBDIR += wise .include diff --git a/biology/py-pydeseq2/Makefile b/biology/py-pydeseq2/Makefile new file mode 100644 index 000000000000..e31c4eb3d0ab --- /dev/null +++ b/biology/py-pydeseq2/Makefile @@ -0,0 +1,26 @@ +PORTNAME= pydeseq2 +DISTVERSION= 0.5.1 +CATEGORIES= biology python +MASTER_SITES= PYPI +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Python implementation of the popular DESeq2 R package +WWW= https://github.com/owkin/PyDESeq2 + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE + +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}anndata>=0.8.0:devel/py-anndata@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}formulaic>=1.0.2:math/py-formulaic@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}formulaic_contrasts>=0.2.0:math/py-formulaic-contrasts@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}matplotlib>=3.6.2:math/py-matplotlib@${PY_FLAVOR} \ + ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}pandas>=1.4.0:math/py-pandas@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scikit-learn>=1.1.0:science/py-scikit-learn@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scipy>1.11.0:science/py-scipy@${PY_FLAVOR} + +USES= python +USE_PYTHON= autoplist distutils + +.include diff --git a/biology/py-pydeseq2/distinfo b/biology/py-pydeseq2/distinfo new file mode 100644 index 000000000000..026ce31f8ca4 --- /dev/null +++ b/biology/py-pydeseq2/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1749586728 +SHA256 (pydeseq2-0.5.1.tar.gz) = 1ec79299f9134748b18bd8242ee4f7f6ccc9407dd18bf32562e051ae5cca626e +SIZE (pydeseq2-0.5.1.tar.gz) = 51390 diff --git a/biology/py-pydeseq2/pkg-descr b/biology/py-pydeseq2/pkg-descr new file mode 100644 index 000000000000..5f4c74926b39 --- /dev/null +++ b/biology/py-pydeseq2/pkg-descr @@ -0,0 +1,4 @@ +PyDESeq2 is a python implementation of the DESeq2 method for +differential expression analysis (DEA) with bulk RNA-seq data, +originally in R. It aims to facilitate DEA experiments for python +users.