Re: Intent to package: molecular biology programs
On Fri, Aug 28, 1998 at 03:17:32PM +0200, Stephane Bortzmeyer wrote:
> - some of these programs are mostly used with *very* huge databases of
> genomes, which are unlikely to be found on any PC (Debian or else)
> machine. Anyone here works in biology?
They're found here. :) Two groups in JCSMR use Debian on the desktop
(Biochem and Human genetics groups), the IT unit has Debian servers.
Databases are served over NFS. There are users in my group who Blast
regularly.
> May be I could draw experience from the people who package other
> scientific sets, but there seems to be very few domain-specific programs
> in Debian?
What I did for Gaussian (we're licensed, it can't be distributed) was
write a 4 line wrapper script (/usr/bin/g94) to set up the environment.
For amber (which has a larger number of entry points) I was considering
extending the wrapper script to set up the amber environment, then exec the
remainder of the arguments.
amber link ...
amber sander ...
This would have the advantage of leaving the names unchanged (put them all
in /usr/lib/amber/bin), keep pollution out of the user's environment
variables, and create only one new script in /usr/bin/ (amber). User's who
didn't want to type 'amber' in front of all amber commands could always add
the /usr/lib/amber/bin path in front of the others or exec the appropriate
.cshrc file (notice how the scientific packages never come with .profiles ?)
This approach would also permit users to have non-csh login shells.
--
Dr. Drake Diedrich, Research Officer - Computing, (02)6279-8302
John Curtin School of Medical Research, Australian National University 0200
Replies to other than Drake.Diedrich@anu.edu.au will be routed off-planet
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