Hi Melanie,
The warning message you get is referring to running an external program to
Artemis (rather than an external site). You can ignore it or change
etc/log4j.properties¹ and remove the #¹ at the start of the line:
log4j.logger.uk.ac.sanger.artemis.ExternalProgram=DEBUG, R
To get error messages open the Show Log Window¹ in the Options¹ menu in
the initial start up window in Artemis. It may prove easier to debug the
script by running it from the command line, e.g.:
etc/run_blastp blastp/blastp_file_of_filenames.18 %U
For the control+V problem, I haven¹t seen that before. What flavour of UNIX
are you using and what version of Java? You could try getting the latest
Java if you haven¹t already.
Regards
Tim Carver
On 20/2/08 08:57, Duffield Melanie L [EMAIL PROTECTED] wrote:
Hi,
I am trying to get Artemis v9 set up on a networked Unix computer (or at
least co-ordinate with our IT people to do this). I have it running locally
on a stand-alone but we want to make it more widely available. I now have
Artemis runnng but still have some problems.
Firstly, I get the messages
log4j:WARN No appenders could be found for logger
(uk.ac.sanger.artemis.ExternalProgram0.
log4j:WARN Please initialize the log4j system properly.
Due to our firewire, we can not set up the program to access any external
sites so is there a way to remove this message?
Secondly I am trying to get blast searches to run. We have local databases
set up under a directory that runs the local windows version of blast and the
blastall is located in the standalone program version. I have edited options
and run_blastp to these two address.
When I start a Blastp search, the sequence file is written out to the blastp
directory and the message 'blastp process received signal: 2 Ok' comes up but
there is no .out file and it seems that blastp doesn't actually run. Is there
any way to see error messages (ie if it can't find or access the database or
blastall). I have checked for typos and access problems and cant see anything
obvious.
Finally, when I use control V to view selected feature, the dialogue box is
put behind the main Artemis window, can I change the default some where to
open it at the front.
Apologies that there are so many questions but maybe someone out there has
seen something like this before and knows the fixes?
Thanks in advance
Melanie Duffield
Team Leader - Advanced DNA and Protein Technologies
Dstl
Rm 201, Bld 7a
Porton Down
Wilts
SP4 0JQ
+44 (0) 1980 614364
The Information contained in this E-Mail and any subsequent correspondence
is private and is intended solely for the intended recipient(s).
For those other than the recipient any disclosure, copying, distribution,
or any action taken or omitted to be taken in reliance on such information
is
prohibited and may be unlawful.
___
Artemis-users mailing list
Artemis-users@sanger.ac.uk
http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
___
Artemis-users mailing list
Artemis-users@sanger.ac.uk
http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
