Subject: pkgsrc paper and bioinformatics packages
To: None <>
From: None <>
List: tech-pkg
Date: 09/22/2003 22:44:15
A group of us at NMSU have been working on collecting a large set of
bioinformatics packages for pkgsrc.  These include almost everything
mentioned in one of the O'Reilly bioinformatics books, a bunch of GIS
software (a new category) from, and some other goodies.
Close to 100 packages in all.

In addition, I have written a paper about this effort that I hope to
have published in the journal Bioinformatics.  If successful, that
will no doubt bring a fair amount of recognition to the pkgsrc system
and may help make it the option of choice for scientific computing.

There remain a couple of steps to finishing this project off and
getting on to the next step.  For those I would like to enlist your
help to whatever degree possible.

First, a copy of the manuscript is available at

Note that it is written from the perspective of the following
yet-to-occur events actually happening.  Consequently, it is not quite
accurate in some details and is not really ready for full public
distribution.  I hope that there is enough interest to work quickly
through those so the paper can be submitted.

Second, I would greatly appreciate any constructive comments on the
paper so that it can be as effective as possible.  Please review the
paper for inaccuracies and areas lacking clarity or in need of
improvement (positive comments are welcome, too :).  There is no need
to burden the entire mailing list with specific comments, so please
direct them to me at

Third, I think it makes sense to incorporate these packages into the
NetBSD pkgsrc repository before I submit the paper.  That will ensure
that they are fully available to anyone interested.  At this point
they all compile perfectly through a bulk build and many have been
run-time tested and installed as binary packages on other machines.
Thus, I forsee few problems with integration, though additional review
is always appreciated.  We are currently in the process of submitting
send-pr requests for existing packages that need to be upgraded, and
of committing the rest to pkgsrc-wip.  I hope that someone will
recognize the value of this work and take on the task of committing it
to the main repository.  Perhaps anyone interested should contact me
( so that we can coordinate this offline as there are a
number of packages that we have constructed that depend on others we
have constructed.  The process of testing and integration will
probably be more efficient if done in consultation with us.  As I
said, though, everything has been thoroughly tested by us, so with a
bit of guidance things should go smoothly and quickly.

Finally, thanks to all of the pkgsrc team for laying such a great
foundation for this work.  I am already receiving inquiries from other
universities about these packages, so I suspect they will form the
nucleus for a set of new initiatives that may attract funding to keep
adding and expanding on the set.  Bioinformatics is definitely a
growth field, so taking the lead in this area could prove valuable.

I look forward to whatever assistance can be offered to help expedite
the final step of integrating this work into the main repository.

Thanks in advance for your enthusiastic help.