Hi Gowtham
It sounds like it is trying to run searches via a SSH connection. In the
options menu in the initial window that opens check that the option to
send searches via ssh is unchecked.
Regards
Tim
On Tue, 24 Mar 2009, Gowthaman Ramasamy wrote:
That's Cool, Tim. Thanks.
As mentioned in my earlier email I made blast to work under Linux & Art11.
Before I move to webstart and Jar files, I wanted to configure blast with
Mac Art11.
I did edit my run_blastp file under the etc directory and it works very well
with command line. But, When I try to run it from main Artemis window, it is
asking for login details (of what? The system?). But, it does not run
blastall really. I don't see any output.
Where am I going wrong? Any hints Tim?.
I am attaching my run_blastp script here....only change I made is for EXEC.
For the database, I am giving the full path in the RUN->set menu option.
That's how I did for my linux-Art11.
Thanks once again for the reply, I really appreciate it.
Gowtham
SBRI
(/run_blastp
/Users/gramasamy/work/localartWD/blastp/blastp_file_of_filenames.4
/Applications/artemis/Artemis.app/Contents/blast-data/uniprot)
Command line: works great, although complains as following..but does the JOB
Error seen:
Fatal server error:
Server is already active for display 0
If this server is no longer running, remove /tmp/.X0-lock
and start again.
AbortDDX
Quitting Xquartz...
On 3/24/09 11:09 AM, "Tim Carver" <t...@sanger.ac.uk> wrote:
Hi Gowthaman
It can be done. You would need to unwrap your jar file and edit the run
scripts that are in that. Then jar the contents back up. Alternatively,
in the Artemis cvs there is a Makefile that can be used to make the jar
files with:
gmake jar
Regards
Tim
On Tue, 24 Mar 2009, Gowthaman Ramasamy wrote:
Hi All,
I am able to configure my local Artemis installation to work with blast and
local database. But, wondering, Can the same thing be done with "web start
artemis" also.
I understand, the path for the database can be set with RUN menu set
options. How can I make it see the blastp and run_blastp scripts......
Thanks very much in advance,
Gowthaman
SBRI
On 3/18/09 3:35 AM, "Tim Carver" <t...@sanger.ac.uk> wrote:
Hi Rob
You can find documentation for setting up blast/fasta and the databases in
the
Readme.txt in the MacOSX distribution.
You can then edit the run_blast* scripts in Artemis.app/Contents/artemis/etc
and options file if required as per the documentation in the manual:
http://www.sanger.ac.uk/Software/Artemis/v11/manual/runmenu.html
Regards
Tim
On 3/17/09 9:25 PM, "Rob Good" <rtg...@unimelb.edu.au> wrote:
Can someone please point me to a link that will tell me how to configure
run_blast, etc options for Macosx artemis.
Rob Good
Ph. +61 3 8344 2347
Genetics Dept
University of Melbourne
PARKVILLE, Australia
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