diff --git a/biology/biostar-tools/Makefile b/biology/biostar-tools/Makefile index b8cca93134d8..8163303759cf 100644 --- a/biology/biostar-tools/Makefile +++ b/biology/biostar-tools/Makefile @@ -1,86 +1,86 @@ PORTNAME= biostar-tools PORTVERSION= 1.10.1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= biology python MAINTAINER= jwb@FreeBSD.org COMMENT= Meta-port for Biostar Handbook tools WWW= https://www.biostarhandbook.com 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 -# Allow pkg build on non-amd64 systems until sra-tools supports them -.if ${ARCH} == amd64 +# sra-tools is only supported on specific architectures +.if ${ARCH} == amd64 || ${ARCH} == aarch64 RUN_DEPENDS+= sra-tools>0:biology/sra-tools .endif SUB_FILES= biostar-shell PLIST_FILES= bin/biostar-shell do-install: @${MKDIR} ${STAGEDIR}${PREFIX}/bin ${INSTALL_SCRIPT} ${WRKDIR}/biostar-shell ${STAGEDIR}${PREFIX}/bin .include diff --git a/biology/biostar-tools/distinfo b/biology/biostar-tools/distinfo index 2d706e980f0b..04755b578d3c 100644 --- a/biology/biostar-tools/distinfo +++ b/biology/biostar-tools/distinfo @@ -1 +1 @@ -TIMESTAMP = 1638373720 +TIMESTAMP = 1708090899 diff --git a/biology/biostar-tools/pkg-descr b/biology/biostar-tools/pkg-descr index eaf4acea11eb..41a5f646b935 100644 --- a/biology/biostar-tools/pkg-descr +++ b/biology/biostar-tools/pkg-descr @@ -1,16 +1,19 @@ -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 +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 +The handbook instructs the reader 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. You can also +install conda packages on FreeBSD if you wish. For details, see /usr/ports/sysutils/linux-miniconda-installer/pkg-descr + +This meta-package installs all of the tools except emboss to the +default PATH (normally /usr/local/bin) so they just work without any +special environment. Emboss commands are installed to +/usr/local/emboss/bin due to conflicts with other packages. Run +"biostar-shell" to add the emboss commands to your PATH, and simply +exit the shell to return your PATH to normal.