biology/biostar-tools: Meta-port for Biostar Handbook tools
Biostar-Tools is a metaport for installing all the tools necessary to work
through the Biostar Handbook, except for bedGrapToBigWig, which has license
restrictions. If you need bedGraphToBigWig, run
cd /usr/ports/biology/ucsc-userapps && make install clean
This commit is contained in:
Jason W. Bacon
parent
98807e08be
commit
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6 changed files with 126 additions and 0 deletions
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@ -14,6 +14,7 @@
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SUBDIR += biolibc
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SUBDIR += bioparser
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SUBDIR += biosoup
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SUBDIR += biostar-tools
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SUBDIR += bolt-lmm
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SUBDIR += bowtie
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SUBDIR += bowtie2
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59
biology/biostar-tools/Makefile
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59
biology/biostar-tools/Makefile
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PORTNAME= biostar-tools
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PORTVERSION= 0.9.0
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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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# sra-tools is almost complete and will be added pending testing
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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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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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USES= metaport python
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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.mk>
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1
biology/biostar-tools/distinfo
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1
biology/biostar-tools/distinfo
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TIMESTAMP = 1624053283
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29
biology/biostar-tools/files/biostar-shell.in
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29
biology/biostar-tools/files/biostar-shell.in
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#!/bin/sh -e
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ucsc_bin=%%PREFIX%%/userapps/bin
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emboss_bin=%%PREFIX%%/emboss/bin
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cat << EOM
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Adding $ucsc_bin and $emboss_bin to \$PATH.
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UCSC kent utils and emboss contain commands that conflict with other tools,
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including at least "calc", "mktime", and "stringify".
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The other commands with these names may serve entirely different functions
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and will not be accessible while running this shell unless you refer to them
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by their absolute path name (e.g. /usr/local/bin/calc), which is not portable,
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BTW, so don't hard-code such paths into your scripts.
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Type "exit" or "Ctrl+D" to return to your normal shell.
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EOM
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export PATH=${ucsc_bin}:${emboss_bin}:$PATH
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# FIXME: Update shell prompts to include (ucsc-kent)?
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# Invoke the user's chosen shell
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if echo $SHELL | egrep -q '/t?csh'; then
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args='-f'
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fi
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exec $SHELL $args
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18
biology/biostar-tools/pkg-descr
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18
biology/biostar-tools/pkg-descr
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Biostar-Tools is a metaport for installing all the tools necessary to work
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through the Biostar Handbook, except for bedGrapToBigWig, which has license
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restrictions. If you need bedGraphToBigWig, run
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cd /usr/ports/biology/ucsc-userapps && make install clean
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The handbook instructs the user to install these tools mostly via bioconda,
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which then requires the user to activate the bioconda environment each time
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they want to use the tools. This meta-package installs all of the tools
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except emboss to the default PATH so they just work without any special
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environment. Emboss commands are installed to /usr/local/emboss/bin due to
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conflicts with other packages.
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You can also install conda packages on FreeBSD. For details, see
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/usr/ports/sysutils/linux-miniconda-installer/pkg-descr
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WWW: https://www.biostarhandbook.com
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18
biology/biostar-tools/pkg-message
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18
biology/biostar-tools/pkg-message
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[
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{ type: install
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message: <<EOM
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If you need bedGraphToBigWig, run:
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cd ${PORTSDIR}/biology/ucsc-userapps && make install clean
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sra-tools is using Linux compatibility for now, until the native FreeBSD
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port is complete.
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For a quick and proper configuration, run the following:
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pkg install -y auto-admin
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auto-install-linux_base
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EOM
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}
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]
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