Hi Gowtham >From the small Artemis window which opens, go to the Options menu and turn off the option to 'Send Searches via SSH'. However, as the etc/run_blast* scripts are wrapped in the jar you will probably need your own custom web launch page so that it has your (non-sanger) setup.
Regards Tim On 4/6/11 6:28 PM, "Gowthaman Ramasamy" <gowthaman.ramas...@seattlebiomed.org> wrote: > Hi Tim, > A related question. > I was able to set up a local blast database, and managed to configure > .artemis_options file to customize artemis. It works when I use locally > installed (linux) version of artemis. But, when I call Webstart version from > sanger, it picks up the .artemis_options nicely (and displays custom db in > Run->blastp menu). But, when I launch the blastp job, it opens a SSH login > window. Is there a way to force run_blastp script to run locally. Or is it not > allowed in webstart version? > > > Log file pasted below. > > Thanks, > Gowtham > > 06 Apr 06:36 - 1.6.0_22 > 06 Apr 06:36 - Apple Inc. > 06 Apr 06:36 - > /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home > 06 Apr 06:36 - Mac OS X > 06 Apr 06:36 - Max. Heap Memory / Mb: 834 > 06 Apr 06:36 - Starting application: Artemis > 06 Apr 06:36 - Diana.ini not found > 06 Apr 06:36 - options not found > 06 Apr 06:36 - options.txt not found > 06 Apr 06:36 - options.text not found > 06 Apr 06:36 - /Users/gramasamy/.artemis_options options read > 06 Apr 06:36 - Working directory: /Users/gramasamy > while reading from LmjF.01.embl: misc_feature can't have ID as a qualifier > 06 Apr 06:36 - PRODUCT STORED AS A CV (product_cv=yes) IN genedb_products > 06 Apr 06:36 - SYNONYM NAMES ARE STORED IN genedb_synonym_type > 06 Apr 06:36 - BAM & VCF not visible > 06 Apr 06:37 - WRITTEN > /Users/gramasamy/Downloads/test/blastp/blastp_file_of_filenames.9 > 06 Apr 06:37 - GET READY TO CALL SSH CLIENT blastp > 06 Apr 06:37 - CALL SSH CLIENT blastp > 06 Apr 06:37 - WRITTEN > /Users/gramasamy/Downloads/test/blastp/blastp_file_of_filenames.10 > 06 Apr 06:37 - GET READY TO CALL SSH CLIENT blastp > 06 Apr 06:37 - CALL SSH CLIENT blastp > while reading from LmjF.01.embl: misc_feature can't have ID as a qualifier > 06 Apr 09:13 - BAM & VCF not visible > 06 Apr 09:13 - WRITTEN > /Users/gramasamy/Downloads/test/blastp/blastp_file_of_filenames.11 > 06 Apr 09:13 - GET READY TO CALL SSH CLIENT blastp > 06 Apr 09:13 - CALL SSH CLIENT blastp > > > > > On 3/16/11 5:04 AM, "Tim Carver" <t...@sanger.ac.uk> wrote: > > Hi Leighton > > Actually using .artemis_options in the users home directory works on > windows, or at least on the windows version I have tried it on here. > > To find where java thinks the user home directory is there is an application > here: > > ftp://ftp.sanger.ac.uk/pub4/resources/software/artemis/util/JavaSystemProps. > jar > > download and double clicking on this will print out the system properties. > One of the properties is 'user.home' which the folder where Artemis should > look for the .artemis_options file. > > I shall update the manual to reflect this. > > Regards > Tim > > On 3/16/11 11:00 AM, "Leighton Pritchard" <leighton.pritch...@scri.ac.uk> > wrote: > >> Hi, >> >> Historically, of the places Artemis can look for an options file, only two >> were available on Windows >> (http://bioweb2.pasteur.fr/docs/artemis/art/options-chapt.html) - one >> requiring repacking of the artemis.jar file, and the other being to place >> the file in the folder containing the artemis.jar file. >> >> When using the Java Web Start version of Artemis on Windows, we can't really >> ask users to unpack and repack the artemis.jar file, but we can put an >> options.txt file in the Downloads folder that contains the artemis.jnlp file >> - this is a little volatile as a solution, though. On OSX the JWS version >> reads my .artemis_options file, happily. >> >> I may have missed it in the documentation, but is there another way to >> specify options when using Java Web Start for Artemis on Windows? >> >> Cheers, >> >> L. >> >> >> -- >> Dr Leighton Pritchard MRSC >> Plant Pathology Programme, SCRI (C block) >> Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA >> e:lpr...@scri.ac.uk w:http://www.scri.ac.uk/staff/leightonpritchard >> gpg/pgp: 0xFEFC205C tel: No telephone during office refurbishment >> >> [The James Hutton Institute logo] >> Please note that from 1 April 2011, SCRI and the Macaulay Land Use Research >> Institute will join to become The James Hutton Institute. >> >> ______________________________________________________ >> SCRI, Invergowrie, Dundee, DD2 5DA. >> The Scottish Crop Research Institute is a charitable company limited by >> guarantee. >> Registered in Scotland No: SC 29367. >> Recognised by the Inland Revenue as a Scottish Charity No: SC 006662. >> >> DISCLAIMER: >> >> This email is from the Scottish Crop Research Institute, but the views >> expressed by the sender are not necessarily the views of SCRI and its >> subsidiaries. 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