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.