Jul 20, 2023

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

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


Checkout these related ports:
  • Wise - Intelligent algorithms for DNA searches
  • Wfa2-lib - Exact gap-affine algorithm using homology to accelerate alignment
  • Vt - Discovers short variants from Next Generation Sequencing data
  • Vsearch - Versatile open-source tool for metagenomics
  • Viennarna - Alignment tools for the structural analysis of RNA
  • Velvet - Sequence assembler for very short reads
  • Vcftools - Tools for working with VCF genomics files
  • Vcflib - C++ library and CLI tools for parsing and manipulating VCF files
  • Vcf2hap - Generate .hap file from VCF for haplohseq
  • Vcf-split - Split a multi-sample VCF into single-sample VCFs
  • Unikmer - Toolkit for nucleic acid k-mer analysis, set operations on k-mers
  • Unanimity - Pacific Biosciences consensus library and applications
  • Ugene - Integrated bioinformatics toolkit
  • Ucsc-userapps - Command line tools from the UCSC Genome Browser project
  • Trimmomatic - Flexible read trimming tool for Illumina NGS data