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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