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Add IGV as an external display application. Contributed by Tobias Wohlfrom.

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Provides two links for IGV:
1) web - to view with Java web start IGV if the user has no IGV installed
2) local - to view in the user's running IGV instance (requires remote port enabled in IGV)
This commit is contained in:
Daniel Blankenberg
2011-03-23 09:57:06 -04:00
parent 7ab9f182dc
commit d95c6b2e52
2 changed files with 71 additions and 0 deletions
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datatypes_conf.xml.sample
+1
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@@ -9,6 +9,7 @@
<converter file="bam_to_summary_tree_converter.xml" target_datatype="summary_tree" depends_on="bai"/>
<display file="ucsc/bam.xml" />
<display file="ensembl/ensembl_bam.xml" />
<!-- <display file="igv/bam.xml" /> -->
</datatype>
<datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true">
<converter file="bed_to_gff_converter.xml" target_datatype="gff"/>
display_applications/igv/bam.xml
+70
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@@ -0,0 +1,70 @@
<display id="igv_bam" version="1.0.0" name="display with IGV">
<link id="web" name="web">
<url>$jnlp.url</url>
<param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" strip_https="True" />
<param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" />
<param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" strip_https="True" mimetype="application/x-java-jnlp-file">&lt;?xml version=&quot;1.0&quot; encoding=&quot;utf-8&quot;?&gt;
&lt;jnlp
spec=&quot;1.0+&quot;
codebase=&quot;http://www.broadinstitute.org/igvdata/jws/prod&quot;&gt;
&lt;information&gt;
&lt;title&gt;IGV 1.5&lt;/title&gt;
&lt;vendor&gt;The Broad Institute&lt;/vendor&gt;
&lt;homepage href=&quot;http://www.broadinstitute.org/igv&quot;/&gt;
&lt;description&gt;IGV Software&lt;/description&gt;
&lt;description kind=&quot;short&quot;&gt;IGV&lt;/description&gt;
&lt;/information&gt;
&lt;security&gt;
&lt;all-permissions/&gt;
&lt;/security&gt;
&lt;resources&gt;
&lt;j2se version=&quot;1.5+&quot; initial-heap-size=&quot;256m&quot; max-heap-size=&quot;1100m&quot;/&gt;
&lt;jar href=&quot;igv.jar&quot; download=&quot;eager&quot; main=&quot;true&quot;/&gt;
&lt;jar href=&quot;batik-codec.jar&quot; download=&quot;eager&quot;/&gt;
&lt;property name=&quot;apple.laf.useScreenMenuBar&quot; value=&quot;true&quot;/&gt;
&lt;property name=&quot;com.apple.mrj.application.growbox.intrudes&quot; value=&quot;false&quot;/&gt;
&lt;property name=&quot;com.apple.mrj.application.live-resize&quot; value=&quot;true&quot;/&gt;
&lt;property name=&quot;com.apple.macos.smallTabs&quot; value=&quot;true&quot;/&gt;
&lt;/resources&gt;
&lt;resources os=&quot;Mac&quot; arch=&quot;i386&quot;&gt;
&lt;property name=&quot;apple.awt.graphics.UseQuartz&quot; value=&quot;false&quot;/&gt;
&lt;nativelib href=&quot;hdfnative-macintel.jar&quot;/&gt;
&lt;/resources&gt;
&lt;resources os=&quot;Mac&quot; arch=&quot;ppc&quot;&gt;
&lt;property name=&quot;apple.awt.graphics.UseQuartz&quot; value=&quot;false&quot;/&gt;
&lt;nativelib href=&quot;hdfnative-macppc.jar&quot;/&gt;
&lt;/resources&gt;
&lt;resources os=&quot;Mac&quot; arch=&quot;PowerPC&quot;&gt;
&lt;property name=&quot;apple.awt.graphics.UseQuartz&quot; value=&quot;false&quot;/&gt;
&lt;nativelib href=&quot;hdfnative-macppc.jar&quot;/&gt;
&lt;/resources&gt;
&lt;resources os=&quot;Windows&quot;&gt;
&lt;property name=&quot;sun.java2d.noddraw&quot; value=&quot;true&quot;/&gt;
&lt;nativelib href=&quot;hdfnative-win.jar&quot;/&gt;
&lt;/resources&gt;
&lt;resources os=&quot;Linux&quot;&gt;
&lt;nativelib href=&quot;hdfnative-linux64.jar&quot;/&gt;
&lt;/resources&gt;
&lt;application-desc main-class=&quot;org.broad.igv.ui.IGVMainFrame&quot;&gt;
&lt;argument&gt;-g&lt;/argument&gt;
&lt;argument&gt;${bam_file.dbkey}&lt;/argument&gt;
&lt;argument&gt;${bam_file.url}&lt;/argument&gt;
&lt;/application-desc&gt;
&lt;/jnlp&gt;
</param>
</link>
<link id="local" name="local">
<url>http://localhost:60151/load?file=${qp($bam_file.url)}&amp;genome=${qp($bam_file.dbkey)}&amp;merge=true</url>
<param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" strip_https="True" />
<param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" />
</link>
</display>