diff --git a/biology/biostar-tools/Makefile b/biology/biostar-tools/Makefile index c0c02c2803c3..912c9de70b84 100644 --- a/biology/biostar-tools/Makefile +++ b/biology/biostar-tools/Makefile @@ -1,77 +1,78 @@ PORTNAME= biostar-tools -PORTVERSION= 1.9.1 +PORTVERSION= 1.10.0 CATEGORIES= biology python MAINTAINER= jwb@FreeBSD.org COMMENT= Meta-port for Biostar Handbook tools LICENSE= BSD2CLAUSE # For a current list see http://data.biostarhandbook.com/install/conda.txt. # Also included are some programs not listed above, but mentioned in the text. # TODO: Add hdfview RUN_DEPENDS= wget>0:ftp/wget \ curl>0:ftp/curl \ nano>0:editors/nano \ parallel>0:sysutils/parallel \ seqkit>0:biology/seqkit \ csvtk>0:science/csvtk \ ${PYTHON_PKGNAMEPREFIX}csvkit>0:textproc/py-csvkit@${PY_FLAVOR} \ miller>0:textproc/miller \ ncbi-entrez-direct>0:biology/ncbi-entrez-direct \ readseq>0:biology/readseq \ snpeff>0:biology/snpeff \ picard-tools>0:biology/picard-tools \ bbmap>0:biology/bbmap \ minimap2>0:biology/minimap2 \ bwa>0:biology/bwa \ bowtie2>0:biology/bowtie2 \ samtools>0:biology/samtools \ emboss>0:biology/emboss \ bedtools>0:biology/bedtools \ bamtools>0:biology/bamtools \ ${PYTHON_PKGNAMEPREFIX}cutadapt>0:biology/py-cutadapt@${PY_FLAVOR} \ seqtk>0:biology/seqtk \ datamash>0:textproc/datamash \ bcftools>0:biology/bcftools \ sra-tools>0:biology/sra-tools \ subread>0:biology/subread \ hisat2>0:biology/hisat2 \ trimmomatic>0:biology/trimmomatic \ fastqc>0:biology/fastqc \ picard-tools>0:biology/picard-tools \ ncbi-blast+>0:biology/ncbi-blast+ \ cd-hit>0:biology/cd-hit \ ${PYTHON_PKGNAMEPREFIX}biopython>0:biology/py-biopython@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pysam>0:biology/py-pysam@${PY_FLAVOR} \ freebayes>0:biology/freebayes \ p5-Net-SSLeay>0:security/p5-Net-SSLeay \ bioawk>0:biology/bioawk \ vt>0:biology/vt \ ${PYTHON_PKGNAMEPREFIX}crossmap>0:biology/py-crossmap@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}goatools>0:biology/py-goatools@${PY_FLAVOR} \ erminej>0:biology/erminej \ ${PYTHON_PKGNAMEPREFIX}ont-fast5-api>0:biology/py-ont-fast5-api@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}multiqc>0:biology/py-multiqc@${PY_FLAVOR} \ flash>0:biology/flash \ bfc:biology/bfc \ Jellyfish>0:biology/jellyfish \ mafft>0:biology/mafft \ clustal-omega>0:biology/clustal-omega \ ${PYTHON_PKGNAMEPREFIX}pywgsim>0:biology/py-pywgsim@${PY_FLAVOR} \ sam2pairwise>0:biology/sam2pairwise \ kallisto>0:biology/kallisto \ bamutil>0:biology/bamutil \ ${PYTHON_PKGNAMEPREFIX}deepTools>0:biology/py-deeptools@${PY_FLAVOR} \ - igv>0:biology/igv + igv>0:biology/igv \ + gffread>0:biology/gffread USES= metaport python SUB_FILES= biostar-shell PLIST_FILES= bin/biostar-shell do-install: @${MKDIR} ${STAGEDIR}${PREFIX}/bin ${INSTALL_SCRIPT} ${WRKDIR}/biostar-shell ${STAGEDIR}${PREFIX}/bin .include diff --git a/biology/biostar-tools/distinfo b/biology/biostar-tools/distinfo index f7fb94ed717f..6155e6419c60 100644 --- a/biology/biostar-tools/distinfo +++ b/biology/biostar-tools/distinfo @@ -1 +1 @@ -TIMESTAMP = 1635607572 +TIMESTAMP = 1636577480