-------- Original Message --------
Dear Kim,
Connie Briggs gave me your email address; she says you've been
invaluable helping her get Artemis to invoke local Blast and Fasta
system calls in Linux.
Here's my question:
Is there something about how Artemis forks its blast process that might
not inherit the .ncbirc from my home directory?
Here's the background:
I am trying to set up another shared Linux workstation at the same
facility and have run into a strange problem, and wonder perhaps if I
describe it here, perhaps you might have some suggestions or insight?
I have downloaded AL591824 from GenBank and formatted it as a nucleic
acid db. Blastall is installed. On the command line I have successfully
tested blastn, querying with the fasta file Artemis generates when it is
told to run a nucleic acid analysis on a selected feature. Normal blast
results are generated.
The same exact command, when invoked by Artemis from run_blastn returns
a "[blastall] FATAL ERROR: FindPath failed" error. A Google search for
similar strings turns up numerous references to not having the .ncbirc
file configured right, and/or in the right place. .ncbirc *is* in the
right place (my home directory), which is why the blast command runs
from the command line.
And so this brings me back to my question: Is there something different
about how Artemis forks its blast process that might not inherit the
.ncbirc from my home directory? Or is it possible that there is some
other problem not related to .ncbirc?
I'm attaching a copy of the run_blastn script that I modified for
debugging purposes; it literally calls the same exact blastall command
I used at the command line (no variables, nothing fancy) and yet returns
an error while blastall at the command line behaves as expected. Connie
says she hasn't noticed this problem before.
As you can tell, I'm quite mystified about this, and as you are The
Artemis Woman, I figured you would probably be the best person to ask.
Thanks in advance for any enlightenment you can provide!
anja
--
Angela M. Baldo, PHD
Microbial Food Safety
ERRC, NAA
ARS, USDA
600 East Mermaid Lane
Wyndmoor, PA 19038-8598
[EMAIL PROTECTED]
voice: (215) 233-6587
fax: (215) 233-6581
run_blastn
Description: application/java-vm
