This might actually generate soft file with raw & supplemental data.

[htsworkflow.git] / encode_submission / geo_gather.py

diff --git a/encode_submission/geo_gather.py b/encode_submission/geo_gather.py
index a2901058371ecec871224076f94362a3eaf6ce43..f9b07ab775a4491226db9c9b97215ea82f7cc54e 100644 (file)
--- a/encode_submission/geo_gather.py
+++ b/encode_submission/geo_gather.py
@@ -58,9 +58,7 @@ def main(cmdline=None):
     model = get_model(opts.model, opts.db_path)
     mapper = None
     if opts.name:
-        mapper = GEOSubmission(opts.name,  model)
-        if opts.library_url is not None:
-            mapper.library_url = opts.library_url
+        mapper = GEOSubmission(opts.name,  model, host=opts.host)
         submission_uri = get_submission_uri(opts.name)
 
 
@@ -77,12 +75,16 @@ def main(cmdline=None):
         results.make_tree_from(opts.make_tree_from)
 
     if opts.fastq:
+        logger.info("Building fastq extraction scripts")
         flowcells = os.path.join(opts.sequence, 'flowcells')
         extractor = CondorFastqExtract(opts.host, flowcells,
+                                       model=opts.model,
                                        force=opts.force)
         extractor.create_scripts(results)
 
     if opts.scan_submission:
+        if opts.name is None:
+            parser.error("Please define a submission name")
         mapper.scan_submission_dirs(results)
 
     if opts.make_soft: