| Port details on branch 2022Q2 |
- biostar-tools Meta-port for Biostar Handbook tools
- 1.10.1_3 biology
 =0      1.10.1_3Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2021-06-18 22:00:16
- Last Update: 2024-02-16 13:42:11
- Commit Hash: 306ace3
- Also Listed In: python
- License: NA
- WWW:
- https://www.biostarhandbook.com
- Description:
- 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 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.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- biostar-tools>0:biology/biostar-tools
- To install the port:
- cd /usr/ports/biology/biostar-tools/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/biostar-tools
- pkg install biostar-tools
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: biostar-tools
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1708090899
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- python3.9 : lang/python39
- Test dependencies:
-
- python3.9 : lang/python39
- Runtime dependencies:
-
- wget>0 : ftp/wget
- curl>0 : ftp/curl
- nano>0 : editors/nano
- parallel>0 : sysutils/parallel
- seqkit>0 : biology/seqkit
- csvtk>0 : science/csvtk
- py39-csvkit>0 : textproc/py-csvkit@py39
- 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
- py39-cutadapt>0 : biology/py-cutadapt@py39
- 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
- py39-biopython>0 : biology/py-biopython@py39
- py39-pysam>0 : biology/py-pysam@py39
- freebayes>0 : biology/freebayes
- p5-Net-SSLeay>0 : security/p5-Net-SSLeay
- bioawk>0 : biology/bioawk
- vt>0 : biology/vt
- py39-crossmap>0 : biology/py-crossmap@py39
- py39-goatools>0 : biology/py-goatools@py39
- erminej>0 : biology/erminej
- py39-ont-fast5-api>0 : biology/py-ont-fast5-api@py39
- py39-multiqc>0 : biology/py-multiqc@py39
- flash>0 : biology/flash
- bfc : biology/bfc
- Jellyfish>0 : biology/jellyfish
- mafft>0 : biology/mafft
- clustal-omega>0 : biology/clustal-omega
- py39-pywgsim>0 : biology/py-pywgsim@py39
- sam2pairwise>0 : biology/sam2pairwise
- kallisto>0 : biology/kallisto
- bamutil>0 : biology/bamutil
- py39-deepTools>0 : biology/py-deeptools@py39
- igv>0 : biology/igv
- gffread>0 : biology/gffread
- python3.9 : lang/python39
- sra-tools>0 : biology/sra-tools
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_biostar-tools
- USES:
- metaport python
- pkg-message:
- For install:
-
If you need bedGraphToBigWig, run:
cd ${PORTSDIR}/biology/ucsc-userapps && make install clean
- Master Sites:
- There is no master site for this port.
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