# HG changeset patch
# User melissacline
# Date 1433282155 25200
# Node ID 154a9b440b63172cd1a1de74d5063b539b72c00f
# Parent  6785e729c7ad275edf9f55f1d0dd907ad2a950ea# Parent  c298bb05640e7e7f6e74104d5a3fcdc5555707b7
Updated the xena jar to version 14, updated the URL of the Xena pages

diff -r 6785e729c7ad -r 154a9b440b63 runXena.py
--- a/runXena.py	Tue Jun 02 14:54:24 2015 -0700
+++ b/runXena.py	Tue Jun 02 14:55:55 2015 -0700
@@ -34,7 +34,7 @@
         while True:
             #Main code goes here ...
             #Note that logger level needs to be set to logging.DEBUG before this shows up in the logs
-            xenaCmdline = "java -jar %s -r %s/files -d %s/db -t %s/tmp --logfile %s/xena.log -p %s -H 0.0.0.0 --no-auto" 
+            xenaCmdline = "java -jar %s -r %s/files -d %s/db -t %s/tmp --logfile %s/xena.log -p %s -H 0.0.0.0" 
             xenaBaseDir = xena.baseDir()
             xenaCmd = xenaCmdline % (xena.jarPath(), xenaBaseDir, 
                                      xenaBaseDir, xenaBaseDir, 
diff -r 6785e729c7ad -r 154a9b440b63 ucsc_xena_datapages.xml
diff -r 6785e729c7ad -r 154a9b440b63 ucsc_xena_hub.xml
diff -r 6785e729c7ad -r 154a9b440b63 ucsc_xenabrowser.xml
diff -r 6785e729c7ad -r 154a9b440b63 xena.jar
diff -r 6785e729c7ad -r 154a9b440b63 xena_import.xml
--- a/xena_import.xml	Tue Jun 02 14:54:24 2015 -0700
+++ b/xena_import.xml	Tue Jun 02 14:55:55 2015 -0700
@@ -32,8 +32,8 @@
     <param format="data" type="data" name="xenaInputData" label="Data to import to Xena" optional="false"/>
     <conditional name="source">
       <param type="select" name="metadataSource" label="Metadata entry">
+	<option value="entry">Enter your own</option>
 	<option value="json">Specify json metadata file</option>
-	<option value="entry">Enter your own</option>
       </param>
       <when value="json">
           <param format="data" type="data" name="xenaMetadata" label="Metadata file" optional="false"/>
@@ -42,8 +42,8 @@
         <param format="str" type="text" name="cohort" label="Cohort" optional="false"/>
         <conditional name="format">
           <param type="select" name="metadataType" label="File Format">
-	    <option value="genomicMatrix">Rows (Identifiers) by Columns (Samples)</option>
-	    <option value="clinicalMatrix">Rows (Samples) by Columns (Identifiers)</option>
+	    <option value="genomicMatrix">Rows (Identifiers) by Columns (Samples) (often genomic data)</option>
+	    <option value="clinicalMatrix">Rows (Samples) by Columns (Identifiers) (often clinical data)</option>
 	    <option value="mutationVector">Mutation By Position</option>
           </param>
           <when value="genomicMatrix">
@@ -57,6 +57,7 @@
 	        <option value="gene expression">gene expression</option>
 	        <option value="gene expression RNAseq">gene expression RNAseq</option>
 	        <option value="gene expression Array">gene expression Array</option>
+	        <option value="mRNA expression">mRNA expression</option>
 	        <option value="somatic mutation (SNP and small INDELs)">somatic mutation (SNP and small INDELs)</option>
 	        <option value="somatic mutation (gene level)">somatic mutation (gene level)</option>
 	        <option value="protein expression RPPA">protein expression RPPA</option>
@@ -72,6 +73,7 @@
 	      <when value="gene expression"/>
 	      <when value="gene expression RNAseq"/>
 	      <when value="gene expression Array"/>
+	      <when value="mRNA expression"/>
 	      <when value="somatic mutation (SNP and small INDELs)"/>
 	      <when value="somatic mutation (gene level)"/>
 	      <when value="protein expression RPPA"/>
@@ -89,6 +91,7 @@
 	        <option value="gene expression">gene expression</option>
 	        <option value="gene expression RNAseq">gene expression RNAseq</option>
 	        <option value="gene expression Array">gene expression Array</option>
+	        <option value="mRNA expression">mRNA expression</option>
 	        <option value="somatic mutation (SNP and small INDELs)">somatic mutation (SNP and small INDELs)</option>
 	        <option value="somatic mutation (gene level)">somatic mutation (gene level)</option>
 	        <option value="protein expression RPPA">protein expression RPPA</option>
@@ -104,6 +107,7 @@
 	      <when value="gene expression"/>
 	      <when value="gene expression RNAseq"/>
 	      <when value="gene expression Array"/>
+	      <when value="mRNA expression"/>
 	      <when value="somatic mutation (SNP and small INDELs)"/>
 	      <when value="somatic mutation (gene level)"/>
 	      <when value="protein expression RPPA"/>
@@ -121,6 +125,6 @@
     <data format="txt" name="outfile"/>
   </outputs>
   <help>
-    To Appear soon...
+    To Appear, soon...
   </help>
 </tool>
diff -r 6785e729c7ad -r 154a9b440b63 xena_utils.pyc