Hi Tim,
I finally solved my problem.
I starded to analyze the run_ scripts and I found they are tailored for
csh SHELL based systems. Ubuntu uses bash.
So I changed the line 32 (e.g. in run_blastx):
EXPANDED_DATABASE=`echo "echo $DATABASE" | /bash/csh -f`
in:
EXPANDED_DATABASE=`echo "echo $DATABASE" | $SHELL -f`
Now all scripts are working. Hope this could help!
Stefano
Tim Carver wrote:
Hi Stefano
No it looks like the script is not getting the database name for some reason
or is loosing it.
The line above the error you have should be:
seq1-out using database swissprot
i.e. should provide the name of the database you are using.
Attached is a run_blastx script that works for me. As you know you need to
define BLATMAT, BLASTDB and the path to blast.
Regards
Tim
On 30/1/07 17:35, "Stefano Ghignone" <[EMAIL PROTECTED]> wrote:
Hi Tim,
thanks for your ready reply.
I tried your suggestion, but it doesn't work...(I think I also tried
before...)
Well, runnning the old run_ script from terminal I get (same as v.8):
[EMAIL PROTECTED]:~/artemis$ run_blastx -onefile seq1.txt seq1-out.txt
swissprot
about to start blastall with input from seq1.txt and output to
seq1-out.txt using database
[blastall] ERROR: No argument given for Database
so I think the problem is that the script doesn't find the database
swissprot!
...even if I create a DATABASE environment variable with the same value
as BLASTDB...
Any other idea?
Stefano
Tim Carver wrote:
Hi Stefano
I think you can probably just copy 'etc/run_blastp' from version 7 to
version 8 then.
Regards
Tim
On 30/1/07 16:16, "Stefano Ghignone" <[EMAIL PROTECTED]> wrote:
Dear all,
....ok...I need an help!
I have an artemis v.7 working on a FedoraCore3 machine, perfectly
integrated with the blast-2.2.15, so that the blast programs listed in
the run menu are working fine using swissprot, nr, nt, and so on...
Now, I'm trying to work with artemis v.8 on a Ubuntu machine, but I
didn't succed with its integration with blast-2.2.15 (note that the
stand alone blast and the artemis itself are working!)
On this machine I have copied the same configuration (blast, artemis,
artemis/etc in my PATH and BLASTDB environment variable) but the run_
commands from the run menu are still not working....
Usually, for e.g., I get this error:
ERROR running blastx:
=================
[blastall] ERROR: No argument given for database
I get the same error even if I run the run_ script from the terminal.
I also tried to specify the database location in the artemis/etc/option :
feature_dna_programs = \
tblastx /usr/BioSW/blast-2.2.15/db \
blastn /usr/BioSW/blast-2.2.15/db \
blastx /usr/BioSW/blast-2.2.15/db \
fastx %uniprot \
clustalx DNA
but with no success again...
It's days I'm working on it......What's wrong?
Cheers
Stefano
--
Dr. Stefano Ghignone
Istituto per la Protezione delle Piante, Sez. Torino - CNR
c/o Dpt. Plant Biology, University of Turin
V.le P.A. Mattioli, 25 phone: +39 011 6705982
I-10125 Turin fax: +39 011 6705962
Italy [EMAIL PROTECTED]
http://www.sppadbase.com
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