# HG changeset patch
# User iuc
# Date 1408277104 14400
# Node ID ffa94ffe1179b94c0f3ff11168a936c1e1c146d6
# Parent  50405cb4f8cdad26069db745b137dbe2ccf1eda8
Uploaded

diff -r 50405cb4f8cd -r ffa94ffe1179 data_manager/data_manager_gemini_download.py
--- a/data_manager/data_manager_gemini_download.py	Sat Aug 16 12:33:49 2014 -0400
+++ b/data_manager/data_manager_gemini_download.py	Sun Aug 17 08:05:04 2014 -0400
@@ -6,11 +6,17 @@
 
 def main():
 
+
+    print sys.argv[1]
     params = json.loads( open( sys.argv[1] ).read() )
+    print 'KKKKKKKKKKKKKK',params
     target_directory = params[ 'output_data' ][0]['extra_files_path']
     os.mkdir( target_directory )
     data_manager_dict = { 'data_tables': {'gemini_databases': [ {'value': sys.argv[2], 'name': sys.argv[3], 'path': target_directory }] } }
 
+    with open(os.path.join(target_directory, 'help.txt'), 'w+') as h:
+        h.write('##############')
+
      #save info to json file
     with open( sys.argv[1], 'wb' ) as out:
         out.write( json.dumps( data_manager_dict ) )
diff -r 50405cb4f8cd -r ffa94ffe1179 data_manager/data_manager_gemini_download.xml
--- a/data_manager/data_manager_gemini_download.xml	Sat Aug 16 12:33:49 2014 -0400
+++ b/data_manager/data_manager_gemini_download.xml	Sun Aug 17 08:05:04 2014 -0400
@@ -4,7 +4,6 @@
         <requirement type="package" version="0.9.1">gemini</requirement>
     </requirements>
     <command interpreter="python">
-        #from galaxy.util.json import from_json_string, to_json_string
 
         ##\$GEMINI_ROOT_DIR/gemini/gemini/install-data.py /home/bag/test/gdata/ $gerp_bp $cadd_score
         data_manager_gemini_download.py "$out_file" "foo" "bar"
diff -r 50405cb4f8cd -r ffa94ffe1179 data_manager_conf.xml
--- a/data_manager_conf.xml	Sat Aug 16 12:33:49 2014 -0400
+++ b/data_manager_conf.xml	Sun Aug 17 08:05:04 2014 -0400
@@ -7,9 +7,9 @@
         <column name="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->
         <column name="path" output_ref="out_file" >
           <move type="directory" relativize_symlinks="True">
-            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">gemini/data</target>
+            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">gemini/data/${value}/${path}</target>
           </move>
-          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/gemini/data</value_translation>
+          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/gemini/data/${value}/${path}</value_translation>
           <value_translation type="function">abspath</value_translation>
         </column>
       </output>
diff -r 50405cb4f8cd -r ffa94ffe1179 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Sat Aug 16 12:33:49 2014 -0400
+++ b/tool_data_table_conf.xml.sample	Sun Aug 17 08:05:04 2014 -0400
@@ -1,6 +1,6 @@
 <tables>
     <table name="gemini_databases" comment_char="#">
-        <columns>value, name</columns>
+        <columns>value, name, path</columns>
         <file path="tool-data/gemini_databases.loc" />
     </table>
 </tables>
diff -r 50405cb4f8cd -r ffa94ffe1179 tool_dependencies.xml
--- a/tool_dependencies.xml	Sat Aug 16 12:33:49 2014 -0400
+++ b/tool_dependencies.xml	Sun Aug 17 08:05:04 2014 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="gemini" version="0.9.1">
-        <repository changeset_revision="610ebefc0db1" name="package_gemini_0_9_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="a10ebb5a71bb" name="package_gemini_0_9_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>