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
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> 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
>>
>>
>>
>
run_blastp
Description: Binary data
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