# HG changeset patch
# User fubar
# Date 1711838009 0
# Node ID 2bdb748df0988cc84c96c42f211905915faca990
# Parent  e26a8a6d2d2ea3c314414d99c7a2b8684a42f4c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 9d5e563dde653450723415b0fccd2ebb4b82477e

diff -r e26a8a6d2d2e -r 2bdb748df098 autogenJB2.py
--- a/autogenJB2.py	Sat Mar 30 07:15:04 2024 +0000
+++ b/autogenJB2.py	Sat Mar 30 22:33:29 2024 +0000
@@ -175,6 +175,8 @@
                             "gff3",
                             "vcf",
                             "maf",
+                            "bed",
+                            "hic"
                         ]:
                             default_session_data["visibility"]["default_on"].append(key)
                         else:
diff -r e26a8a6d2d2e -r 2bdb748df098 jbrowse2.py
--- a/jbrowse2.py	Sat Mar 30 07:15:04 2024 +0000
+++ b/jbrowse2.py	Sat Mar 30 22:33:29 2024 +0000
@@ -1106,6 +1106,13 @@
     def add_paf(self, data, trackData, pafOpts, **kwargs):
         tname = trackData["name"]
         tId = trackData["label"]
+        url = "%s.paf" % tId
+        useuri = data.startswith("http://") or data.startswith("https://")
+        if not useuri:
+            dest = "%s/%s" % (self.outdir, url)
+            self.symlink_or_copy(os.path.realpath(data), dest)
+        else:
+            url = data
         categ = trackData["category"]
         pgnames = [
             x.strip() for x in pafOpts["genome_label"].split(",") if len(x.strip()) > 0
@@ -1119,7 +1126,6 @@
             % (pafOpts, pgnames, pgpaths, tId)
         )
         for i, gname in enumerate(pgnames):
-            lab = trackData["label"]
             if len(gname.split()) > 1:
                 gname = gname.split()[0]
             passnames.append(gname)
@@ -1127,19 +1133,13 @@
             useuri = pgpaths[i].startswith("http://") or pgpaths[i].startswith(
                 "https://"
             )
-            if not useuri:
-                url = "%s.paf" % (lab)
-            else:
-                url = data
+
             if gname not in self.genome_names:
                 # ignore if already there - eg for duplicates among pafs.
                 asstrack = self.make_assembly(pgpaths[i], gname, useuri)
                 self.genome_names.append(gname)
                 self.tracksToAdd[gname] = []
                 self.assemblies.append(asstrack)
-                if not useuri:
-                    dest = "%s/%s" % (self.outdir, url)
-                    self.symlink_or_copy(os.path.realpath(data), dest)
         trackDict = {
             "type": "SyntenyTrack",
             "trackId": tId,
@@ -1156,16 +1156,19 @@
             "displays": [
                 {
                     "type": "LGVSyntenyDisplay",
-                    "displayId": "%s-LGVSyntenyDisplay" % lab,
+                    "displayId": "%s-LGVSyntenyDisplay" % tId,
                 },
-                {"type": "DotplotDisplay", "displayId": "%s-DotplotDisplay" % lab},
+                {
+                    "type": "DotplotDisplay",
+                    "displayId": "%s-DotplotDisplay" % tId,
+                },
                 {
                     "type": "LinearComparativeDisplay",
-                    "displayId": "%s-LinearComparativeDisplay" % lab,
+                    "displayId": "%s-LinearComparativeDisplay" % tId,
                 },
                 {
                     "type": "LinearSyntenyDisplay",
-                    "displayId": "%s-LinearSyntenyDisplay" % lab,
+                    "displayId": "%s-LinearSyntenyDisplay" % tId,
                 },
             ],
         }
@@ -1173,7 +1176,7 @@
             "displays": [
                 {
                     "type": "LGVSyntenyDisplay",
-                    "displayId": "%s-LGVSyntenyDisplay" % lab,
+                    "displayId": "%s-LGVSyntenyDisplay" % tId,
                 }
             ]
         }
@@ -1343,9 +1346,9 @@
                 drdict = {
                     "reversed": False,
                     "assemblyName": gnome,
-                    "start": 1,
+                    "start": 0,
                     "end": 100000,
-                    "refName": refName
+                    "refName": refName,
                 }
                 ddl = default_data.get("defaultLocation", None)
                 if ddl:
@@ -1383,10 +1386,10 @@
             session_json["views"] = session_views
         else:
             session_json["views"] += session_views
-
+        pp = json.dumps(session_views, indent=2)
         config_json["defaultSession"] = session_json
         self.config_json.update(config_json)
-
+        logging.debug("defaultSession=%s" % (pp))
         with open(self.config_json_file, "w") as config_file:
             json.dump(self.config_json, config_file, indent=2)