Scripts for automatically distributing DNA sequencer data to user
directories are available.
The campus DNA sequencing facility recently closed. As we no longer
need to maintain "security by obscurity" on this software I'm
making it available to anybody who wants it. It consists of
a script we used for automatically pulling data off of the workstation
which drove a 3730 sequencer and distributing it out to user directories
for subsequent pickup. There are also scripts for cleaning up and
directions for making archives. While not a thing of beauty, these all
all worked quite reliably for us. However, it is important that the
syntax of the filenames and directories generated by the ABI base
calling software be matched to the script, and depending on how your ABI
calling software is configured, you'll probably have to make a few minor
tweaks.
We also have software for calling bases and preparing views of the
sequences for web access. Unfortunately this uses some GCG software,
so I can't distribute that code until it is rewritten to use EMBOSS
programs instead.
Anyway, here are the scripts for anybody who wants them:
ftp://saf.bio.caltech.edu/pub/software/molbio/distribute_dna_data.tar.gz
Regards,
David Mathog
mathog from caltech.edu
