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
_______________________________________________
Artemis-users mailing list
Artemis-users@sanger.ac.uk
http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
