[BiO BB] FreeBSD in bioinformatics

Johann Visagie johann at egenetics.com
Mon Mar 12 10:04:55 EST 2001

Hi everyone,

There has been some discussion on this list lately about the use of various
free Unix operating systems in bioinformatics.  I hope that what follows is
therefore not too far off-topic.

Some list members may be interested to know that there is a small but
concerted effort underway by FreeBSD users in bioinformatics (and other
bioscientific computing fields) to add as many applications as possible to
the FreeBSD ports tree.

The FreeBSD ports tree has gained some fame even outside the FreeBSD (and
BSD) communities as one excellent way of integrating third party applications
into a Unix-based operating system.  It goes somewhat beyond a packaging
system (such as RedHat's RPM) and encompasses all levels of a user's normal
interaction with a package to get it up and running - from download through
patching, compilation and installation.  The closest equivalent in the Linux
world is (I believe) Debian's apt-get system.

Some of the reasons why we're doing this:

- A more "bio-friendly" free Unix sounds like a good idea!  :-)

- End users:  What can be easier than:
  "cd /usr/ports/biology/<package-name>; make install"  to install just about
  any bioinformatics package.

- System administrators:  I'm in a position where I can appreciate the pain
  of running a network of diverse boxes for bioinformatics research.  The
  ports tree provides me with the tools to automate tasks such as the
  updating of software packages.  Installing and cleanly deinstalling
  packages becomes trivial.  Finding out which versions of the dozens of
  cascaded dependencies (libraries, etc.) of a large package are required -
  and downloading and installing them - simply isn't a problem anymore.  It
  all happens automatically.  

- We found that there are already a number of FreeBSD users in bioscientific
  fields.  We're trying to encourage them not to "hack in a vacuum" - i.e.
  instead of just spending days trying to get some obscure package to work
  on your system, do the little bit of extra work and submit a port of it.
  Every user of the OS will immediately benefit by being able to install said
  package easily, and if one of them finds a better way of doing it, the
  patches will be submitted back to you, making *your* life easier.  The open
  source principle applied to mass system administration.  :-)

- Since the ports structure is closely integrated with the operating system,
  and since the operating system in question is one which ships with all the
  tools for building distributions, I foresee that we may eventually be able
  to produce a simple, free CD distribution that installs both the OS and all
  tools needed by a bioinformaticist.  (This may or may not prove desirable -
  but it's an idea I have...)

- There is a lot of talk about creating a unified ports structure across the
  various BSD-based operating systems.  This will include Apple's next-
  generation operating system, MacOS X.  And Macs are of course still
  entrenched in academia in many parts of the world.

- Like Linux, FreeBSD supports the Compaq Alpha architecture (which is of
  course quite popular in this field).  The ports system allows for
  cross-platform ports.  What we need is more FreeBSD Alpha users to test the
  cross-platform operation of our bio ports on the Alpha.  (And goodness
  knows, anything is better than Tru64! :-> )

Anyone who finds the above interesting, or any FreeBSD users in the field who
want to share experiences, please feel free to join our mailing list:


-- Johann

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