FYI, FreeBSD users can now install all the bioinformatics software referenced by the Biostar Handbook via FreeBSD ports. Everything except bedGraphToBigWig can be installed simply by running
pkg install biostar-tools
bedGraphToBigWig is part of ucsc-userapps, which cannot be redistributed for licensing reasons, so there is no binary package. However, the FreeBSD ports system allows installing from source as easily as from a binary package (though it will take much longer), so restrictive licenses are not a major hurdle. ucsc-userapps can be easily installed separately by running
cd /usr/ports/biology/ucsc-userapps && make install
This will prompt you to accept the license terms and then automatically download from UCSC, build, and install.
Note that these installations are an alternative to conda/pip. If you have installed via FreeBSD ports/packages, you can skip all of the conda/pip commands in the handbook.
All programs are installed into the default PATH (/usr/local/bin) except for emboss and ucsc-userapps, which have multiple command-name conflicts with other programs. To use emboss commands, add /usr/local/emboss/bin to your PATH:
For Bourne-shell derivatives: (sh, bash, dash, zsh, …)
For C-shell derivatives: (csh, tcsh)
setenv PATH /usr/local/emboss/bin:$PATH
Or from any shell, you can run a separate shell process with the augmented PATH rather than hack the environment of your current shell:
env PATH=/usr/local/emboss/bin:$PATH bash
Replace “bash” with the shell of your choice. Then simply exit the shell to restore your previous PATH.
For UCSC-userapps, add /usr/local/bin/userapps.
The ports also install convenience scripts ucsc-shell and emboss-shell for quickly enabling the tools for interactive use. These scripts run a sub-shell with the proper directory prepended to PATH.
For anyone who is not a FreeBSD user but interested in trying it out, I would recommend GhostBSD for Unix novices. It’s very much like Ubuntu Linux with a graphical installer and management tools.
For the more Unix-savvy, there is also the desktop-installer app, which adds virtually any desktop environment to a stock FreeBSD system:
Please report any problems with biostar-tools or other FreeBSD ports on the FreeBSD site:
Questions posted on this forum may never be seen by the right people.
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