# HG changeset patch
# User sanbi-uwc
# Date 1457335671 18000
# Node ID a9b725202132b5a532268558aac7dc765418e657
# Parent  68b7023c6a2ffe40836fab80a325b13d2080f953
planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 9ea1c9c5fdf0ed65170469f809b81ba9e82f91d3

diff -r 68b7023c6a2f -r a9b725202132 data_manager/novocraft_index_builder.py
--- a/data_manager/novocraft_index_builder.py	Sat Mar 05 10:29:02 2016 -0500
+++ b/data_manager/novocraft_index_builder.py	Mon Mar 07 02:27:51 2016 -0500
@@ -37,26 +37,19 @@
     elif not os.path.exists(target_directory):
         os.mkdir(target_directory)
 
-    if 'GALAXY_SLOTS' in os.environ:
-        nslots = os.environ['GALAXY_SLOTS']
-    else:
-        nslots = 1
+    index_filename = os.path.join(target_directory,"%.nix" % sequence_id)
+    cmdline_str = 'novoindex {} {}'.format(index_filename, fasta_filename)
+    cmdline = shlex.split(cmdline_str)
 
-    #cmdline_str = 'STAR --runMode genomeGenerate --genomeDir {} --genomeFastaFiles {} --runThreadN {}'.format(
-    #    target_directory,
-    #    fasta_filename,
-    #    nslots)
-    #cmdline = shlex.split(cmdline_str)
-    index_filename = 'foo'
-    cmdline = ('touch', '{}/{}'.format(target_directory, index_filename))
+    #index_filename = 'foo'
+    #cmdline = ('touch', '{}/{}'.format(target_directory, index_filename))
     try:
         check_call(cmdline)
     except CalledProcessError:
         print("Error building RNA STAR index", file=sys.stderr)
 
-    data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=os.path.join(target_directory, index_filename) )
+    data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=index_filename )
     _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
-    return ( index_filename )
 
 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
     data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
diff -r 68b7023c6a2f -r a9b725202132 data_manager_conf.xml
--- a/data_manager_conf.xml	Sat Mar 05 10:29:02 2016 -0500
+++ b/data_manager_conf.xml	Mon Mar 07 02:27:51 2016 -0500
@@ -8,9 +8,7 @@
                 <column name="name" />
                 <column name="path" output_ref="out_file">
                     <move type="file">
-                        <!--<move type="directory" relative_symlinks="True"> -->
                         <!-- no need to set source, gets taken from out_dir.extra_files_path -->
-                         <source>${path}</source> <!-- File name within the extra files path -->
                         <target base="${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>