diff --git a/biology/Makefile b/biology/Makefile index 25eba238a6ad..606e1982ee9b 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,189 +1,190 @@ COMMENT = Biology SUBDIR += abyss SUBDIR += ad2vcf SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += bioawk SUBDIR += biococoa SUBDIR += biolibc SUBDIR += bioparser SUBDIR += biosoup 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 += 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 += molden SUBDIR += mopac SUBDIR += mothur SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit 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 += 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-gtfparse SUBDIR += py-hits SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-multiqc SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pandas-charm SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += py-scikit-bio SUBDIR += py-xenaPython SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += rampler 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 += seqio SUBDIR += seqtk SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += spoa SUBDIR += stacks SUBDIR += star SUBDIR += stringtie SUBDIR += subread SUBDIR += tRNAscan-SE SUBDIR += tabixpp SUBDIR += treekin SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene 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-crossmap/Makefile b/biology/py-crossmap/Makefile new file mode 100644 index 000000000000..7946de949b5e --- /dev/null +++ b/biology/py-crossmap/Makefile @@ -0,0 +1,21 @@ +PORTNAME= crossmap +DISTVERSION= 0.5.2 +CATEGORIES= biology python +MASTER_SITES= CHEESESHOP +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} +DISTNAME= CrossMap-${DISTVERSION} + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Lift over genomics coordinates between assemblies + +LICENSE= GPLv2 +LICENSE_FILE= ${WRKSRC}/LICENSE.txt + +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pysam>0:biology/py-pysam@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}bx-python>0:biology/py-bx-python@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pyBigWig>0:biology/py-bigwig@${PY_FLAVOR} + +USES= python:3.5+ +USE_PYTHON= autoplist cython distutils + +.include diff --git a/biology/py-crossmap/distinfo b/biology/py-crossmap/distinfo new file mode 100644 index 000000000000..e78c67b1ddcf --- /dev/null +++ b/biology/py-crossmap/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1617575391 +SHA256 (CrossMap-0.5.2.tar.gz) = d996c7a17ca2665903d7bfa4ca67d35c37c800e1ce3129ed1274e65504b93d69 +SIZE (CrossMap-0.5.2.tar.gz) = 10866811 diff --git a/biology/py-crossmap/files/patch-lib_cmmodule_twoList.py b/biology/py-crossmap/files/patch-lib_cmmodule_twoList.py new file mode 100644 index 000000000000..efbb0c474374 --- /dev/null +++ b/biology/py-crossmap/files/patch-lib_cmmodule_twoList.py @@ -0,0 +1,18 @@ +--- lib/cmmodule/twoList.py.orig 2021-04-04 22:42:53 UTC ++++ lib/cmmodule/twoList.py +@@ -5,7 +5,7 @@ from operator import mul,add,sub + def check_list(v1,v2): + '''check if the length of two list is same''' + if v1.size != v2.size: +- raise ValueError,"the lenght of both arrays must be the same" ++ raise ValueError("the length of both arrays must be the same") + pass + + def Add(v1,v2): +@@ -50,4 +50,4 @@ def Min(v1,v2): + def euclidean_distance(v1,v2): + '''return euclidean distance''' + check_list(v1,v2) +- return (sum((v1.__sub__(v2))**2) / v1.size)**0.5 +\ No newline at end of file ++ return (sum((v1.__sub__(v2))**2) / v1.size)**0.5 diff --git a/biology/py-crossmap/files/patch-setup.py b/biology/py-crossmap/files/patch-setup.py new file mode 100644 index 000000000000..4fa46ca7cc20 --- /dev/null +++ b/biology/py-crossmap/files/patch-setup.py @@ -0,0 +1,10 @@ +--- setup.py.orig 2021-04-05 15:27:07 UTC ++++ setup.py +@@ -11,7 +11,6 @@ def main(): + setup( name = "CrossMap", + version = "0.5.2", + python_requires='>=3.5', +- py_modules = [ 'psyco_full' ], + packages = find_packages( 'lib' ), + package_dir = { '': 'lib' }, + package_data = { '': ['*.ps'] }, diff --git a/biology/py-crossmap/pkg-descr b/biology/py-crossmap/pkg-descr new file mode 100644 index 000000000000..dfb768a40775 --- /dev/null +++ b/biology/py-crossmap/pkg-descr @@ -0,0 +1,6 @@ +CrossMap is a program for genome coordinates conversion between different +assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used +file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF, MAF VCF, +and gVCF. + +WWW: https://pypi.python.org/pypi/crossmap