[Bio-software] scripts for automatically distributing DNA sequencer data to user directories

David Mathog via bio-soft%40net.bio.net (by mathog from caltech.edu)
Wed Mar 14 18:22:28 EST 2007


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



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