remove self.usejson

reorder displays for bed so the pileup is no longer default - was useful when no bigwig available but that will be fixed shortly.
galaxyproject · Jan 19, 2024 · 1b7e6ba · 1b7e6ba
1 parent 906bfc0
commit 1b7e6ba
Showing 1 changed file with 5 additions and 7 deletions.
diff --git a/tools/jbrowse2/jbrowse2.py b/tools/jbrowse2/jbrowse2.py
@@ -375,7 +375,6 @@ def metadata_from_node(node):
 
 class JbrowseConnector(object):
     def __init__(self, outdir, genomes):
-        self.usejson = True
         self.giURL = GALAXY_INFRASTRUCTURE_URL
         self.outdir = outdir
         os.makedirs(self.outdir, exist_ok=True)
@@ -930,14 +929,14 @@ def add_bed(self, data, ext, trackData):
                 },
             },
             "displays": [
-                {
-                    "type": "LinearPileupDisplay",
-                    "displayId": "%s-LinearPileupDisplay" % tId,
-                },
                 {
                     "type": "LinearBasicDisplay",
                     "displayId": "%s-LinearBasicDisplay" % tId,
                 },
+                {
+                    "type": "LinearPileupDisplay",
+                    "displayId": "%s-LinearPileupDisplay" % tId,
+                },
                 {"type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId},
             ],
         }
@@ -1427,8 +1426,7 @@ def parse_style_conf(item):
         jc.add_general_configuration(general_data)
     x = open(args.xml, "r").read()
     jc.config_json["tracks"] = jc.tracksToAdd
-    if jc.usejson:
-        jc.write_config()
+    jc.write_config()
     jc.add_default_session(default_session_data)
 
     # jc.text_index() not sure what broke here.