Hi Preethi There is some general JNLP documentation online if you search for jnlp syntax¹. For Artemis arguments and properties, you may find it useful to download some of the JNLP files on that webpage and start with those. Below is one of these examples. The properties and arguments are the same as they would be for the command line. For example on the command line to open a BAM file (locally or over http) automatically using the Dbam option:
-Dbam=http://www.genedb.org/artemis/NAR/Malaria_RNASeq/version2.1.4/MAL_8h.b am It assumes the index file (.bai) is in the same place as the BAM file. This is then defined in the JNLP with as a property: <property name=²bam² value=²">http://......²/> <http://......²/> The sequence and annotation files are loaded as arguments (within <argument></argument> tags). To open a sequence and a separate annotation file (e.g. art St.dna + St.embl) the plus sign is a separate argument: <argument>ftp://ftp.sanger.ac.uk/pub/pathogens/st/St.dna</argument> <argument>+</argument> <argument>ftp://ftp.sanger.ac.uk/pub/pathogens/st/St.art</argument> To position the Artemis display at a base position the offset¹ can be defined, e.g.: <property name="offset" value="100800" /> If you keep the codebase line the same I think it should download the most current version from the Sanger. Regards Tim <?xml version="1.0" encoding="UTF-8"?> <jnlp spec="1.0+" codebase="http://www.sanger.ac.uk/resources/software/artemis/java/"; > <information> <title>Artemis</title> <vendor>Sanger Institute</vendor> <homepage href="http://www.sanger.ac.uk/resources/software/artemis/"/> <description>Artemis</description> <description kind="short">DNA sequence viewer and annotation tool. </description> <offline-allowed/> </information> <security> <all-permissions/> </security> <resources> <j2se version="1.6+" initial-heap-size="32m" max-heap-size="800m"/> <jar href="sartemis_dev.jar"/> <property name="com.apple.mrj.application.apple.menu.about.name" value="Artemis" /> <property name="artemis.environment" value="UNIX" /> <property name="j2ssh" value="" /> <property name="apple.laf.useScreenMenuBar" value="true" /> <property name="offset" value="100800" /> <property name="bam" value="http://www.genedb.org/artemis/NAR/Malaria_RNASeq/version2.1.4/MAL_8h. bam,http://www.genedb.org/artemis/NAR/Malaria_RNASeq/version2.1.4/MAL_24h.ba m" /> </resources> <application-desc main-class="uk.ac.sanger.artemis.components.ArtemisMain"> <argument>ftp://ftp.sanger.ac.uk/pub4/pathogens/Plasmodium/falciparum/3D7/3D 7.latest_version/December_2010/Pf3D7_01.embl.gz</argument> </application-desc> </jnlp> On 3/19/12 7:20 PM, "PIRA (Preethi Ramaiya)" <p...@novozymes.com> wrote: > Hi > > I would like to be able to serve up genomes with BAM files as shown in > http://www.sanger.ac.uk/resources/software/artemis/ngs/. It is very handy for > our end-users to be able to visualize the a NGS alignments in a familiar tool. > > Is there a how to set up artemis with Webstart and bam files loaded per > genome- how do you get from my genome file and the correspond .bam and .bai to > the jlnp file that is needed by the web start. > > its probably obvious but I am new to web-start and would appreciate any > help. > > The server is running Ubuntu with Apache as the web server. It is set up with > the right mime types for Java Webstart. > > > Thank you > Preethi > > > > Best Regards > Preethi Ramaiya > > > > > > _______________________________________________ > Artemis-users mailing list > Artemis-users@sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
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