# HG changeset patch
# User fubar
# Date 1711703699 0
# Node ID 7230a2422507884dace5fb54d876c59c316360d2
# Parent  c4eb6a85db70bef4bd5c87fcc4c596958cd7cea0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2c7d6c19a42c421de987ebfdf927c64062ebd79f-dirty

diff -r c4eb6a85db70 -r 7230a2422507 autogenJB2.py
--- a/autogenJB2.py	Fri Mar 29 07:27:20 2024 +0000
+++ b/autogenJB2.py	Fri Mar 29 09:14:59 2024 +0000
@@ -204,9 +204,13 @@
             for gnome in jc.genome_names:
                 trackconf += jc.tracksToAdd[gnome]
             logging.warn(
-                "^^%% adding trackconf=%s for gnome %s" % (trackconf, gnome)
+                "++++ adding trackconf=%s for gnome %s" % (trackconf, gnome)
             )
             jc.config_json["tracks"] = trackconf
+            assconf = jc.config_json.get("assemblies", [])
+            assconf += jc.assemblies
+            jc.config_json["assemblies"] = assconf
+            logging.warn("+++assemblies=%s, gnames=%s" % (assconf, jc.genome_names))
             jc.write_config()
             default_session_data.update({"session_name": sessName})
             track_conf.update(default_session_data)
diff -r c4eb6a85db70 -r 7230a2422507 jbrowse2.py
--- a/jbrowse2.py	Fri Mar 29 07:27:20 2024 +0000
+++ b/jbrowse2.py	Fri Mar 29 09:14:59 2024 +0000
@@ -1607,13 +1607,14 @@
     }
     jc.add_general_configuration(general_data)
     trackconf = jc.config_json.get("tracks", [])
-    logging.warn("genome_names=%s" % jc.genome_names)
+    logging.warn("%%%%%%%%% genome_names=%s" % jc.genome_names)
     for gnome in jc.genome_names:
         trackconf += jc.tracksToAdd[gnome]
     jc.config_json["tracks"] = trackconf
     assconf = jc.config_json.get("assemblies", [])
     assconf += jc.assemblies
     jc.config_json["assemblies"] = assconf
+    logging.warn("&&&assemblies=%s, gnames=%s" % (assconf, jc.genome_names))
     jc.write_config()
     jc.add_default_session(default_session_data)
     # jc.text_index() not sure what broke here.