diff autogenJB2.py @ 62:ab0d6782a95f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty

--- a/autogenJB2.py	Tue Mar 26 00:52:34 2024 +0000
+++ b/autogenJB2.py	Thu Mar 28 04:51:06 2024 +0000
@@ -68,7 +68,8 @@
             jc = jbC(
                 outdir=args.outdir,
                 jbrowse2path=args.jbrowse2path,
-                genomes=[
+            )
+            genomes=[
                     {
                         "path": x,
                         "label": genome_names[i],
@@ -80,9 +81,8 @@
                     }
                     for i, x in enumerate(genome_paths)
                 ],
-            )
-
-            jc.process_genomes()
+            logging.warn("#!!! paths=%s, genomes=%s" % (genome_paths, genomes))
+            assref_name = jc.process_genomes(genomes[0])
             default_session_data = {
                 "visibility": {
                     "default_on": [],
@@ -96,7 +96,7 @@
             tnames = [x[2] for x in listtracks]
             texts = [x[1] for x in listtracks]
             for i, track in enumerate(listtracks):
-                track_conf = {"trackfiles": [], "category": "autogenerated"}
+                track_conf = {"trackfiles": [], "category": "autogenerated", "assemblyNames": assref_name}
                 tpath, trext, trackname = track[:3]
                 track_conf["dataset_id"] = trackname
                 useuri = "no"