# HG changeset patch
# User fubar
# Date 1705633708 0
# Node ID a26c41e304c3fb7bb64a5a74b339beacf9b6662b
# Parent  9a168aa68f06f6b12d5a3832a558364781474531
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1b7e6ba50013775621cbdfdc101152a7f5c5e15b

diff -r 9a168aa68f06 -r a26c41e304c3 jbrowse2.py
--- a/jbrowse2.py	Thu Jan 18 06:41:25 2024 +0000
+++ b/jbrowse2.py	Fri Jan 19 03:08:28 2024 +0000
@@ -375,7 +375,6 @@
 
 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)
@@ -931,13 +930,13 @@
             },
             "displays": [
                 {
+                    "type": "LinearBasicDisplay",
+                    "displayId": "%s-LinearBasicDisplay" % tId,
+                },
+                {
                     "type": "LinearPileupDisplay",
                     "displayId": "%s-LinearPileupDisplay" % tId,
                 },
-                {
-                    "type": "LinearBasicDisplay",
-                    "displayId": "%s-LinearBasicDisplay" % tId,
-                },
                 {"type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId},
             ],
         }
@@ -1427,8 +1426,7 @@
         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.