wip/biostar-tools 1.10.1 NetBSD
Meta-package for Biostar Handbook tools
- System
- NetBSD
- Repository
- pkgsrc-wip
- Maintainer
- [email protected]
- License
- modified-bsd
- Categories
- wip, biology, meta-pkgs
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/pkgsrc/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/pkg/emboss/bin due to conflicts with other packages.
In the other systems
| System | Port | Version |
|---|---|---|
| NetBSD | wip/biostar-tools | 1.10.1 |
| FreeBSD | biology/biostar-tools | 2.1 |
Install
From pkgsrc-wip (no binary package):
cd /usr/pkgsrc/wip/biostar-tools && make install clean
Dependencies
Run dependencies 34
- archivers/lz4
- archivers/xz
- archivers/zstd
- biology/bcftools
- biology/bedtools
- biology/bowtie2
- biology/bwa
- biology/cdhit
- biology/fastqc
- biology/gffread
- biology/hisat2
- biology/igv
- biology/kallisto
- biology/minimap2
- biology/ncbi-blast+
- biology/py-biopython
- biology/py-cutadapt
- biology/samtools
- biology/seqtk
- biology/sra-tools
- biology/trimmomatic
- editors/nano
- net/wget
- parallel/parallel
- textproc/csvkit
- textproc/miller
- wip/bamtools
- wip/biolibc-tools
- wip/datamash
- wip/fastq-trim
- wip/py-multiqc
- wip/readseq
- wip/subread
- www/curl
No port depends on this one.