Mercurial > repos > iuc > data_manager_gemini_database_downloader

changeset 4:688e5894bb2b draft

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Uploaded
author iuc
date Sun, 17 Aug 2014 09:44:56 -0400
parents 7cfa2506531d
children 839086b394ba
files data_manager/data_manager_gemini_download.py data_manager/data_manager_gemini_download.xml data_manager_conf.xml tool-data/gemini_databases.loc.sample tool_data_table_conf.xml.sample
diffstat 5 files changed, 20 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager_gemini_download.py	Sun Aug 17 08:34:58 2014 -0400
+++ b/data_manager/data_manager_gemini_download.py	Sun Aug 17 09:44:56 2014 -0400
@@ -3,23 +3,28 @@
 import sys
 import os
 import json
+import shlex
 import datetime
 import subprocess
 
 def main():
 
     today = datetime.date.today()
-    print sys.argv[1]
+    gemini_root_dir = os.environ['GEMINI_ROOT_DIR']
     params = json.loads( open( sys.argv[1] ).read() )
-    print 'KKKKKKKKKKKKKK',params
     target_directory = params[ 'output_data' ][0]['extra_files_path']
     os.mkdir( 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']])
-
-    data_manager_dict = { 'data_tables': {'gemini_databases': [ {'value': today.isoformat(), 'name': 'GEMINI annotations (%s)' % today.isoformat(), 'path': target_directory }] } }
+    gemini_exec = os.path.join( gemini_root_dir, 'gemini', 'gemini', 'install-data.py' )
+    cmd = gemini_exec + " %s %s" % (' '.join( [params['param_dict']['gerp_bp'], params['param_dict']['cadd']] ), target_directory)
+    #cmd = gemini_exec + " --help > %s/foo.txt" % target_directory
+    ret = subprocess.check_call( cmd, shell=True )
+    data_manager_dict = { 
+                'data_tables': 
+                    {'gemini_databases': [ 
+                            {'value': today.isoformat(), 'dbkey': 'hg19', 'name': 'GEMINI annotations (%s)' % today.isoformat(), 'path': './%s' % today.isoformat() } 
+                                        ] 
+                    }
+                }
 
     #save info to json file
     with open( sys.argv[1], 'wb' ) as out:
--- a/data_manager/data_manager_gemini_download.xml	Sun Aug 17 08:34:58 2014 -0400
+++ b/data_manager/data_manager_gemini_download.xml	Sun Aug 17 09:44:56 2014 -0400
@@ -10,7 +10,7 @@
         <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" 
+        <param name="gerp_bp" type="boolean" truevalue="--extra gerp_bp" falsevalue="" checked="True" 
             label="Download GERP for GEMINI database annotation" help="(--extra gerp_bp)"/>
     </inputs>
     <outputs>
--- a/data_manager_conf.xml	Sun Aug 17 08:34:58 2014 -0400
+++ b/data_manager_conf.xml	Sun Aug 17 09:44:56 2014 -0400
@@ -4,12 +4,13 @@
         <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="dbkey" /> <!-- 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>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">gemini/data/${dbkey}/${value}</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/gemini/data/${value}</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/gemini/data/${dbkey}/${value}</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
--- a/tool-data/gemini_databases.loc.sample	Sun Aug 17 08:34:58 2014 -0400
+++ b/tool-data/gemini_databases.loc.sample	Sun Aug 17 09:44:56 2014 -0400
@@ -1,3 +1,3 @@
 ## GEMINI databases
-#Version	Description	Path
-#08_08_2014	Database (08-08-2014)	/data/0/gemini/08_08_2014/
+#Version	dbkey	Description
+#08_08_2014	hg19	Database (08-08-2014)
--- a/tool_data_table_conf.xml.sample	Sun Aug 17 08:34:58 2014 -0400
+++ b/tool_data_table_conf.xml.sample	Sun Aug 17 09:44:56 2014 -0400
@@ -1,6 +1,6 @@
 <tables>
     <table name="gemini_databases" comment_char="#">
-        <columns>value, name, path</columns>
+        <columns>value, dbkey, name, path</columns>
         <file path="tool-data/gemini_databases.loc" />
     </table>
 </tables>