# HG changeset patch
# User melissacline
# Date 1409785344 25200
# Node ID cae2b765ca5d8fa18f2475954c02edfce65df79b
# Parent  b3cd322f77490b789b83965ad1715d97faeb3617
Changing how the Xena base dir is communicated

diff -r b3cd322f7749 -r cae2b765ca5d tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Sep 03 15:34:45 2014 -0400
+++ b/tool_dependencies.xml	Wed Sep 03 16:02:24 2014 -0700
@@ -4,7 +4,8 @@
     <install version="1.0">
       <actions>
 	<action type="set_environment">
-          <environment_variable name="XENA_BASE_DIR" action="set_to">$INSTALL_DIR/xena</environment_variable>
+          <environment_variable name="XENA_BASE_DIR" action="set_to">${__tool_d\
+ata_path__}/shared//xena</environment_variable>
         </action>
       </actions>
     </install>
diff -r b3cd322f7749 -r cae2b765ca5d xena_import.py
--- a/xena_import.py	Wed Sep 03 15:34:45 2014 -0400
+++ b/xena_import.py	Wed Sep 03 16:02:24 2014 -0700
@@ -17,9 +17,10 @@
     parser.add_argument("genomicDataPathname", type=str)
     parser.add_argument("cohort", type=str)
     parser.add_argument("type", type=str)
-    parser.add_argument("xenaInputDir", type=str)
     args = parser.parse_args()
 
+    xenaBaseDir = os.getenv("XENA_BASE_DIR", "~")
+
     # Assemble the metadata in JSON format
     metadata = { 'cohort': args.cohort, 'type': args.type }
     jsonMetadata = json.dumps(metadata, indent=2) 
diff -r b3cd322f7749 -r cae2b765ca5d xena_import.xml
--- a/xena_import.xml	Wed Sep 03 15:34:45 2014 -0400
+++ b/xena_import.xml	Wed Sep 03 16:02:24 2014 -0700
@@ -4,7 +4,7 @@
     <requirement type="package" version="1.0">installXena2</requirement>
   </requirements>
   <command interpreter="python">
-    xena_import.py ${xenaInputData} ${cohort} ${metadataType} ${XENA_BASE_DIR}/files/
+    xena_import.py ${xenaInputData} ${cohort} ${metadataType} 
   </command>
   <inputs>
     <param format="data" type="data" name="xenaInputData" label="Data to import to Xena" optional="false"/>