# HG changeset patch
# User sanbi-uwc
# Date 1457433532 18000
# Node ID 283eec05d1de6865ef6deead12a3c0c32d5d99cf
# Parent  a9b725202132b5a532268558aac7dc765418e657
planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit e14dbfe322e3787d1ec9b7467a3677b101784227

diff -r a9b725202132 -r 283eec05d1de data_manager/novocraft_index_builder.py
--- a/data_manager/novocraft_index_builder.py	Mon Mar 07 02:27:51 2016 -0500
+++ b/data_manager/novocraft_index_builder.py	Tue Mar 08 05:38:52 2016 -0500
@@ -37,13 +37,14 @@
     elif not os.path.exists(target_directory):
         os.mkdir(target_directory)
 
-    index_filename = os.path.join(target_directory,"%.nix" % sequence_id)
+    print(sequence_id)
+    nix_file = sequence_id + ".nix"
+    index_filename = os.path.join(target_directory, nix_file)
     cmdline_str = 'novoindex {} {}'.format(index_filename, fasta_filename)
     cmdline = shlex.split(cmdline_str)
 
-    #index_filename = 'foo'
-    #cmdline = ('touch', '{}/{}'.format(target_directory, index_filename))
     try:
+        print(cmdline)
         check_call(cmdline)
     except CalledProcessError:
         print("Error building RNA STAR index", file=sys.stderr)
@@ -83,7 +84,7 @@
 
     params = loads(open(filename).read())
     target_directory = params['output_data'][0]['extra_files_path']
-    os.makedirs(target_directory)
+    #os.makedirs(target_directory)
     data_manager_dict = {}
 
     dbkey, sequence_id, sequence_name = get_dbkey_id_name(params, dbkey_description=args.dbkey_description)
diff -r a9b725202132 -r 283eec05d1de data_manager_conf.xml
--- a/data_manager_conf.xml	Mon Mar 07 02:27:51 2016 -0500
+++ b/data_manager_conf.xml	Tue Mar 08 05:38:52 2016 -0500
@@ -11,7 +11,7 @@
                         <!-- no need to set source, gets taken from out_dir.extra_files_path -->
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/novocraft_index/${value}</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/{$dbkey}/novocraft_index/${value}/${path}</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/novocraft_index/${value}/</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>