diff data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.py @ 4:6f0be85be8fb draft

Uploaded

--- a/data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.py	Thu Oct 27 05:45:31 2016 -0400
+++ b/data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.py	Thu Oct 27 06:49:58 2016 -0400
@@ -156,7 +156,7 @@
 def generate_alfa_indexes(path_to_alfa, gtf_file_name):
     logging.info("____________________________________________________________")
     logging.info("*** Generating alfa indexes from %s" % gtf_file_name)
-    alfa_result = subprocess.Popen(['python', path_to_alfa + 'ALFA.py', '-a',  gtf_file_name], stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+    alfa_result = subprocess.Popen(['python', path_to_alfa, '-a',  gtf_file_name], stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
     alfa_out, alfa_err = alfa_result.communicate()
     if alfa_err != None and not re.search('### End of program', alfa_err):
         msg = 'Generation Failed due an alfa error: %s' % (alfa_err)
@@ -181,8 +181,9 @@
 def main():
     options, args = get_arg()
     galaxy_root_dir = args[0]
+    tool_dir = args[1]
 
-    path_to_alfa = os.path.join(galaxy_root_dir, 'tools/alfa/')
+    path_to_alfa = os.path.join(tool_dir, 'ALFA.py')
     path_to_tmp_dir = os.path.join(galaxy_root_dir, 'database/tmp/')
 
     if options.output_filename == None: