Date: Fri, 18 Jun 2021 21:57:23 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 6df92a09ad7a - main - biology/biostar-tools: Meta-port for Biostar Handbook tools Message-ID: <202106182157.15ILvNPL082210@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=6df92a09ad7a75d3533ac3510cba668c74689255 commit 6df92a09ad7a75d3533ac3510cba668c74689255 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2021-06-18 21:56:23 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2021-06-18 21:56:23 +0000 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 --- biology/Makefile | 1 + biology/biostar-tools/Makefile | 59 ++++++++++++++++++++++++++++ biology/biostar-tools/distinfo | 1 + biology/biostar-tools/files/biostar-shell.in | 29 ++++++++++++++ biology/biostar-tools/pkg-descr | 18 +++++++++ biology/biostar-tools/pkg-message | 18 +++++++++ 6 files changed, 126 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 4acd54fab965..ec9728ced8ee 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -14,6 +14,7 @@ SUBDIR += biolibc SUBDIR += bioparser SUBDIR += biosoup + SUBDIR += biostar-tools SUBDIR += bolt-lmm SUBDIR += bowtie SUBDIR += bowtie2 diff --git a/biology/biostar-tools/Makefile b/biology/biostar-tools/Makefile new file mode 100644 index 000000000000..f9f7023f4ba5 --- /dev/null +++ b/biology/biostar-tools/Makefile @@ -0,0 +1,59 @@ +PORTNAME= biostar-tools +PORTVERSION= 0.9.0 +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. +# sra-tools is almost complete and will be added pending testing +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 \ + 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} + +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 <bsd.port.mk> diff --git a/biology/biostar-tools/distinfo b/biology/biostar-tools/distinfo new file mode 100644 index 000000000000..5eb0b9bcd39d --- /dev/null +++ b/biology/biostar-tools/distinfo @@ -0,0 +1 @@ +TIMESTAMP = 1624053283 diff --git a/biology/biostar-tools/files/biostar-shell.in b/biology/biostar-tools/files/biostar-shell.in new file mode 100755 index 000000000000..275572a3b6c7 --- /dev/null +++ b/biology/biostar-tools/files/biostar-shell.in @@ -0,0 +1,29 @@ +#!/bin/sh -e + +ucsc_bin=%%PREFIX%%/userapps/bin +emboss_bin=%%PREFIX%%/emboss/bin +cat << EOM + +Adding $ucsc_bin and $emboss_bin to \$PATH. + +UCSC kent utils and emboss contain commands that conflict with other tools, +including at least "calc", "mktime", and "stringify". + +The other commands with these names may serve entirely different functions +and will not be accessible while running this shell unless you refer to them +by their absolute path name (e.g. /usr/local/bin/calc), which is not portable, +BTW, so don't hard-code such paths into your scripts. + +Type "exit" or "Ctrl+D" to return to your normal shell. + +EOM + +export PATH=${ucsc_bin}:${emboss_bin}:$PATH + +# FIXME: Update shell prompts to include (ucsc-kent)? + +# Invoke the user's chosen shell +if echo $SHELL | egrep -q '/t?csh'; then + args='-f' +fi +exec $SHELL $args diff --git a/biology/biostar-tools/pkg-descr b/biology/biostar-tools/pkg-descr new file mode 100644 index 000000000000..104c8bdb5efb --- /dev/null +++ b/biology/biostar-tools/pkg-descr @@ -0,0 +1,18 @@ +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 + +The handbook instructs the user to install these tools mostly via bioconda, +which then requires the user to activate the bioconda environment each time +they want to use the tools. This meta-package installs all of the tools +except emboss to the default PATH so they just work without any special +environment. Emboss commands are installed to /usr/local/emboss/bin due to +conflicts with other packages. + +You can also install conda packages on FreeBSD. For details, see + + /usr/ports/sysutils/linux-miniconda-installer/pkg-descr + +WWW: https://www.biostarhandbook.com diff --git a/biology/biostar-tools/pkg-message b/biology/biostar-tools/pkg-message new file mode 100644 index 000000000000..cd4162b88842 --- /dev/null +++ b/biology/biostar-tools/pkg-message @@ -0,0 +1,18 @@ +[ +{ type: install + message: <<EOM + +If you need bedGraphToBigWig, run: + + cd ${PORTSDIR}/biology/ucsc-userapps && make install clean + +sra-tools is using Linux compatibility for now, until the native FreeBSD +port is complete. + +For a quick and proper configuration, run the following: + +pkg install -y auto-admin +auto-install-linux_base +EOM +} +]
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