70e9e19c3c
Only sra-tools is still non-portable, but it will take some time to add support for other architectures. In the meantime, allow aarch64 and powerpc64 users to have a biostar-tools package.
84 lines
2.7 KiB
Makefile
84 lines
2.7 KiB
Makefile
PORTNAME= biostar-tools
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PORTVERSION= 1.10.1
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CATEGORIES= biology python
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MAINTAINER= jwb@FreeBSD.org
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COMMENT= Meta-port for Biostar Handbook tools
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LICENSE= BSD2CLAUSE
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# For a current list see http://data.biostarhandbook.com/install/conda.txt.
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# Also included are some programs not listed above, but mentioned in the text.
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# TODO: Add hdfview
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RUN_DEPENDS= wget>0:ftp/wget \
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curl>0:ftp/curl \
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nano>0:editors/nano \
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parallel>0:sysutils/parallel \
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seqkit>0:biology/seqkit \
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csvtk>0:science/csvtk \
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${PYTHON_PKGNAMEPREFIX}csvkit>0:textproc/py-csvkit@${PY_FLAVOR} \
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miller>0:textproc/miller \
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ncbi-entrez-direct>0:biology/ncbi-entrez-direct \
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readseq>0:biology/readseq \
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snpeff>0:biology/snpeff \
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picard-tools>0:biology/picard-tools \
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bbmap>0:biology/bbmap \
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minimap2>0:biology/minimap2 \
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bwa>0:biology/bwa \
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bowtie2>0:biology/bowtie2 \
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samtools>0:biology/samtools \
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emboss>0:biology/emboss \
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bedtools>0:biology/bedtools \
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bamtools>0:biology/bamtools \
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${PYTHON_PKGNAMEPREFIX}cutadapt>0:biology/py-cutadapt@${PY_FLAVOR} \
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seqtk>0:biology/seqtk \
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datamash>0:textproc/datamash \
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bcftools>0:biology/bcftools \
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subread>0:biology/subread \
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hisat2>0:biology/hisat2 \
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trimmomatic>0:biology/trimmomatic \
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fastqc>0:biology/fastqc \
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picard-tools>0:biology/picard-tools \
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ncbi-blast+>0:biology/ncbi-blast+ \
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cd-hit>0:biology/cd-hit \
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${PYTHON_PKGNAMEPREFIX}biopython>0:biology/py-biopython@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}pysam>0:biology/py-pysam@${PY_FLAVOR} \
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freebayes>0:biology/freebayes \
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p5-Net-SSLeay>0:security/p5-Net-SSLeay \
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bioawk>0:biology/bioawk \
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vt>0:biology/vt \
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${PYTHON_PKGNAMEPREFIX}crossmap>0:biology/py-crossmap@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}goatools>0:biology/py-goatools@${PY_FLAVOR} \
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erminej>0:biology/erminej \
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${PYTHON_PKGNAMEPREFIX}ont-fast5-api>0:biology/py-ont-fast5-api@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}multiqc>0:biology/py-multiqc@${PY_FLAVOR} \
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flash>0:biology/flash \
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bfc:biology/bfc \
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Jellyfish>0:biology/jellyfish \
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mafft>0:biology/mafft \
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clustal-omega>0:biology/clustal-omega \
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${PYTHON_PKGNAMEPREFIX}pywgsim>0:biology/py-pywgsim@${PY_FLAVOR} \
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sam2pairwise>0:biology/sam2pairwise \
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kallisto>0:biology/kallisto \
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bamutil>0:biology/bamutil \
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${PYTHON_PKGNAMEPREFIX}deepTools>0:biology/py-deeptools@${PY_FLAVOR} \
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igv>0:biology/igv \
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gffread>0:biology/gffread
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USES= metaport python
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.include <bsd.port.pre.mk>
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# Allow pkg build on non-amd64 systems until sra-tools supports them
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.if ${ARCH} == amd64
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RUN_DEPENDS+= sra-tools>0:biology/sra-tools
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.endif
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SUB_FILES= biostar-shell
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PLIST_FILES= bin/biostar-shell
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do-install:
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@${MKDIR} ${STAGEDIR}${PREFIX}/bin
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${INSTALL_SCRIPT} ${WRKDIR}/biostar-shell ${STAGEDIR}${PREFIX}/bin
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.include <bsd.port.post.mk>
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