diff --git a/datatypes_conf.xml.sample b/datatypes_conf.xml.sample index b2f8fee4391..6e5030f54b4 100644 --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -9,6 +9,7 @@ + diff --git a/display_applications/igv/bam.xml b/display_applications/igv/bam.xml new file mode 100644 index 00000000000..03c1bbf3543 --- /dev/null +++ b/display_applications/igv/bam.xml @@ -0,0 +1,70 @@ + + + $jnlp.url + + + <?xml version="1.0" encoding="utf-8"?> +<jnlp + spec="1.0+" + codebase="http://www.broadinstitute.org/igvdata/jws/prod"> + <information> + <title>IGV 1.5</title> + <vendor>The Broad Institute</vendor> + <homepage href="http://www.broadinstitute.org/igv"/> + <description>IGV Software</description> + <description kind="short">IGV</description> + </information> + <security> + <all-permissions/> + </security> + <resources> + +<j2se version="1.5+" initial-heap-size="256m" max-heap-size="1100m"/> + <jar href="igv.jar" download="eager" main="true"/> + <jar href="batik-codec.jar" download="eager"/> + <property name="apple.laf.useScreenMenuBar" value="true"/> + <property name="com.apple.mrj.application.growbox.intrudes" value="false"/> + <property name="com.apple.mrj.application.live-resize" value="true"/> + <property name="com.apple.macos.smallTabs" value="true"/> + </resources> + + <resources os="Mac" arch="i386"> + <property name="apple.awt.graphics.UseQuartz" value="false"/> + <nativelib href="hdfnative-macintel.jar"/> + </resources> + + <resources os="Mac" arch="ppc"> + <property name="apple.awt.graphics.UseQuartz" value="false"/> + <nativelib href="hdfnative-macppc.jar"/> + </resources> + + <resources os="Mac" arch="PowerPC"> + <property name="apple.awt.graphics.UseQuartz" value="false"/> + <nativelib href="hdfnative-macppc.jar"/> + </resources> + + <resources os="Windows"> + <property name="sun.java2d.noddraw" value="true"/> + <nativelib href="hdfnative-win.jar"/> + </resources> + + <resources os="Linux"> + <nativelib href="hdfnative-linux64.jar"/> + </resources> + + <application-desc main-class="org.broad.igv.ui.IGVMainFrame"> + <argument>-g</argument> + <argument>${bam_file.dbkey}</argument> + <argument>${bam_file.url}</argument> + </application-desc> +</jnlp> + + + + + + http://localhost:60151/load?file=${qp($bam_file.url)}&genome=${qp($bam_file.dbkey)}&merge=true + + + +