New biostar-tools metaport for FreeBSD

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, …)

export PATH=/usr/local/emboss/bin:$PATH

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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