changeset 3:7cfa2506531d draft

Uploaded

--- a/data_manager/data_manager_gemini_download.py	Sun Aug 17 08:05:04 2014 -0400
+++ b/data_manager/data_manager_gemini_download.py	Sun Aug 17 08:34:58 2014 -0400
@@ -3,21 +3,25 @@
 import sys
 import os
 import json
+import datetime
+import subprocess
 
 def main():
 
-
+    today = datetime.date.today()
     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 }] } }
+    target_directory = os.path.join( target_directory, today.isoformat() )
+    os.mkdir( target_directory )
+    print target_directory
+    subprocess.check_call(["$GEMINI_ROOT_DIR/gemini/gemini/install-data.py", target_directory, params['param_dict']['gerp_bp'], params['param_dict']['cadd']])
 
-    with open(os.path.join(target_directory, 'help.txt'), 'w+') as h:
-        h.write('##############')
+    data_manager_dict = { 'data_tables': {'gemini_databases': [ {'value': today.isoformat(), 'name': 'GEMINI annotations (%s)' % today.isoformat(), 'path': target_directory }] } }
 
-     #save info to json file
+    #save info to json file
     with open( sys.argv[1], 'wb' ) as out:
         out.write( json.dumps( data_manager_dict ) )
 

--- a/data_manager/data_manager_gemini_download.xml	Sun Aug 17 08:05:04 2014 -0400
+++ b/data_manager/data_manager_gemini_download.xml	Sun Aug 17 08:34:58 2014 -0400
@@ -4,29 +4,14 @@
         <requirement type="package" version="0.9.1">gemini</requirement>
     </requirements>
     <command interpreter="python">
-
-        ##\$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"
-
-        ##silent open( "${out_file}", 'wb' ).write( to_json_string( $data_manager_dict ) )
-
-##        data_manager_snpEff_download.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar --config \$SNPEFF_JAR_PATH/snpEff.config 
-##        #if $snpDb.genomeSrc == "named":
-##          --genome_version "${snpDb.genome_version}"
-##        #else
-##          --genome_version "${snpDb.genome_databases.fields.value}"
-##          --organism "${snpDb.genome_databases.fields.name}"
-##        #end if
-##        "$out_file"
-        </command>
+        data_manager_gemini_download.py "$out_file"
+    </command>
     <inputs>
-
         <param name="cadd" type="boolean" truevalue="--extra cadd_score" falsevalue="" checked="True" 
             label="Download CADD scores for GEMINI database annotation" help="(--extra cadd_score)"/>
 
         <param name="gerp_bp" type="boolean" truevalue="--extra cadd_score" falsevalue="" checked="True" 
             label="Download GERP for GEMINI database annotation" help="(--extra gerp_bp)"/>
-
     </inputs>
     <outputs>
            <data name="out_file" format="data_manager_json" label="${tool.name}"/>

--- a/data_manager_conf.xml	Sun Aug 17 08:05:04 2014 -0400
+++ b/data_manager_conf.xml	Sun Aug 17 08:34:58 2014 -0400
@@ -1,20 +1,20 @@
 <?xml version="1.0"?>
 <data_managers>
-  <data_manager tool_file="data_manager/data_manager_gemini_download.xml" id="data_manager_gemini_download" >
-    <data_table name="gemini_databases">  <!-- Defines a Data Table to be modified. -->
-      <output> <!-- Handle the output of the Data Manager Tool -->
-        <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
-        <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="${GALAXY_DATA_MANAGER_DATA_PATH}">gemini/data/${value}/${path}</target>
-          </move>
-          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/gemini/data/${value}/${path}</value_translation>
-          <value_translation type="function">abspath</value_translation>
-        </column>
-      </output>
-    </data_table>
-  </data_manager>
+    <data_manager tool_file="data_manager/data_manager_gemini_download.xml" id="data_manager_gemini_download" >
+        <data_table name="gemini_databases">  <!-- Defines a Data Table to be modified. -->
+            <output> <!-- Handle the output of the Data Manager Tool -->
+                <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+                <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="${GALAXY_DATA_MANAGER_DATA_PATH}">gemini/data/${value}</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/gemini/data/${value}</value_translation>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+            </output>
+        </data_table>
+    </data_manager>
 </data_managers>