# HG changeset patch
# User chrisw
# Date 1573536265 18000
# Node ID 1032e2599a5e469ac07b1aad7e0b4d6fce6ad7c3
# Parent 5615f4cee039af421b0eeea71ad8841e49039588
Uploaded
diff -r 5615f4cee039 -r 1032e2599a5e data_manager_monorail_index/data_manager/data_manager.py
--- a/data_manager_monorail_index/data_manager/data_manager.py Mon Nov 11 23:38:27 2019 -0500
+++ b/data_manager_monorail_index/data_manager/data_manager.py Tue Nov 12 00:24:25 2019 -0500
@@ -19,11 +19,17 @@
def main(args):
workdir = os.path.join(os.getcwd(), 'monorail_index')
data_manager_entry = {}
+ ref = args.url.split('/')[-1]
if args.name is None:
- args.name = args.url.split('/')[-1]
+ args.name = ref
data_manager_entry['value'] = args.name.lower()
data_manager_entry['name'] = args.name
- data_manager_entry['path'] = args.output
+ jsonin = open(args.output).read()
+ sys.stderr.write(jsonin)
+ params = json.loads(jsonin)
+ target_directory = params['output_data'][0]['extra_files_path']
+ data_manager_entry['path'] = params['output_data'][0]['extra_files_path']
+ data_manager_entry['exons_path'] = data_manager_entry['path'] + os.sep + ref + os.sep + 'gtf' + os.sep + 'exons.bed'
data_manager_json = dict(data_tables=dict(monorail_index=data_manager_entry))
file(args.output, 'w').write(json.dumps(data_manager_json))
diff -r 5615f4cee039 -r 1032e2599a5e data_manager_monorail_index/data_manager_conf.xml
--- a/data_manager_monorail_index/data_manager_conf.xml Mon Nov 11 23:38:27 2019 -0500
+++ b/data_manager_monorail_index/data_manager_conf.xml Tue Nov 12 00:24:25 2019 -0500
@@ -8,6 +8,7 @@
+