diff --git a/biology/Makefile b/biology/Makefile index d02ab1ac20eb..081fb65708b1 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,210 +1,211 @@ 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 += biosig 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-PySCeS 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-python-libsbml 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 += sigviewer 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-PySCeS/Makefile b/biology/py-PySCeS/Makefile new file mode 100644 index 000000000000..a399b65938fc --- /dev/null +++ b/biology/py-PySCeS/Makefile @@ -0,0 +1,38 @@ +PORTNAME= PySCeS +DISTVERSION= 0.9.8post1 +DISTVERSIONSUFFIX= -31-g28dd259 +CATEGORIES= biology python +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Python Simulator for Cellular Systems + +LICENSE= BSD2CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE.txt + +PY_DEPENDS= ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}ipython>0:devel/ipython@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}nose>0:devel/py-nose@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}python-libsbml>0:biology/py-python-libsbml@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} +BUILD_DEPENDS= ${PY_DEPENDS} +RUN_DEPENDS= ${PY_DEPENDS} + +USES= fortran python +USE_PYTHON= distutils autoplist + +USE_GITHUB= yes +GH_PROJECT= ${PORTNAME:tl} + +LDFLAGS+= -lpython${PYTHON_VER} -shared # see https://github.com/PySCeS/pysces/issues/29 + +post-install: + @${STRIP_CMD} \ + ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pysces/pitcon/pitcon.cpython-38.so \ + ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pysces/nleq2/nleq2.cpython-38.so + +do-test: install # from section 2.1 Loading PySCeS in http://pysces.sourceforge.net/pdf/userguide.pdf + @${PYTHON_CMD} -c "import pysces; pysces.test();" + +.include diff --git a/biology/py-PySCeS/distinfo b/biology/py-PySCeS/distinfo new file mode 100644 index 000000000000..5eb6ca09af67 --- /dev/null +++ b/biology/py-PySCeS/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1629133609 +SHA256 (PySCeS-pysces-0.9.8post1-31-g28dd259_GH0.tar.gz) = e8634ae766331b57dcc697a4a59c8c2844e744a63e47727a15b4a7f5e32c537d +SIZE (PySCeS-pysces-0.9.8post1-31-g28dd259_GH0.tar.gz) = 2670650 diff --git a/biology/py-PySCeS/pkg-descr b/biology/py-PySCeS/pkg-descr new file mode 100644 index 000000000000..72ca017a7c61 --- /dev/null +++ b/biology/py-PySCeS/pkg-descr @@ -0,0 +1,3 @@ +PySCeS provides a variety of tools for the analysis of cellular systems. + +WWW: http://pysces.sourceforge.net/