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PORTNAME= biostar-tools
PORTVERSION= 1.10.1
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 \
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 \
gffread>0:biology/gffread
USES= metaport python
.include <bsd.port.pre.mk>
# Allow pkg build on non-amd64 systems until sra-tools supports them
.if ${ARCH} == amd64
RUN_DEPENDS+= sra-tools>0:biology/sra-tools
.endif
SUB_FILES= biostar-shell
PLIST_FILES= bin/biostar-shell
do-install:
@${MKDIR} ${STAGEDIR}${PREFIX}/bin
${INSTALL_SCRIPT} ${WRKDIR}/biostar-shell ${STAGEDIR}${PREFIX}/bin
.include <bsd.port.post.mk>
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