diff --git a/tools/jbrowse2/jbrowse2.py b/tools/jbrowse2/jbrowse2.py
index b8a0024a4b..f2ae4cac13 100644
--- a/tools/jbrowse2/jbrowse2.py
+++ b/tools/jbrowse2/jbrowse2.py
@@ -10,6 +10,7 @@
 import re
 import shutil
 import ssl
+import string
 import struct
 import subprocess
 import tempfile
@@ -20,7 +21,7 @@
 logging.basicConfig(level=logging.DEBUG)
 log = logging.getLogger("jbrowse")
 
-JB2VER = "v2.12.3"
+JB2VER = "v2.15.4"
 # version pinned if cloning - but not cloning now
 logCommands = True
 # useful for seeing what's being written but not for production setups
@@ -419,7 +420,7 @@ def __init__(self, outdir, jbrowse2path):
         self.tracksToAdd = {}
         self.config_json = {}
         self.config_json_file = os.path.join(outdir, "config.json")
-        self.clone_jbrowse()
+        self.clone_jbrowse(realclone=False)
 
     def get_cwd(self, cwd):
         if cwd:
@@ -620,18 +621,9 @@ def text_index(self):
         # Index tracks
         args = [
             "jbrowse",
-            "text-index",
-            "--target",
-            self.outdir,
-            "--assemblies",
-            self.genome_name,
+            "text-index"
         ]
-
-        tracks = ",".join(self.trackIdlist)
-        if tracks:
-            args += ["--tracks", tracks]
-
-            self.subprocess_check_call(args)
+        self.subprocess_check_call(args)
 
     def add_hic(self, data, trackData):
         """
@@ -1555,7 +1547,7 @@ def clone_jbrowse(self, realclone=False):
 
         """
         dest = self.outdir
-        if realclone:
+        if (not os.path.exists(self.jbrowse2path)) or realclone:
             self.subprocess_check_call(
                 ["jbrowse", "create", dest, "-f", "--tag", f"{JB2VER}"]
             )
@@ -1600,7 +1592,9 @@ def parse_style_conf(item):
     args = parser.parse_args()
     tree = ET.parse(args.xml)
     root = tree.getroot()
-
+    removeMe = string.punctuation.replace('.', ' ').replace('/', '').replace('-', '')
+    # first is a space because space needs to be added here for removal from labels as paths.
+    nopunct = str.maketrans(dict.fromkeys(removeMe))
     # This should be done ASAP
     GALAXY_INFRASTRUCTURE_URL = root.find("metadata/galaxyUrl").text
     # Sometimes this comes as `localhost` without a protocol
@@ -1617,7 +1611,7 @@ def parse_style_conf(item):
         genomes = [
             {
                 "path": x.attrib["path"],
-                "label": x.attrib["label"].split(" ")[0].replace(",", ""),
+                "label": x.attrib["label"].split(" ")[0].translate(nopunct),
                 "useuri": x.attrib["useuri"],
                 "meta": metadata_from_node(x.find("metadata")),
             }
@@ -1655,7 +1649,7 @@ def parse_style_conf(item):
                     if x.attrib['ext'] == "bed":
                         isBed = True
                     track_conf["label"] = "%s_%d" % (
-                        x.attrib["label"].replace(" ", "_").replace(",", "_").replace("/", "_"),
+                        x.attrib["label"].translate(nopunct),
                         trackI,
                     )
                     trackI += 1
@@ -1663,7 +1657,7 @@ def parse_style_conf(item):
                     if is_multi_bigwig:
                         multi_bigwig_paths.append(
                             (
-                                track_conf["label"],
+                                track_conf["label"].translate(nopunct),
                                 track_conf["useuri"],
                                 os.path.realpath(x.attrib["path"]),
                             )
@@ -1770,4 +1764,5 @@ def parse_style_conf(item):
     jc.write_config()
     # note that this can be left in the config.json but has NO EFFECT if add_defsess_to_index is called.
     # jc.add_defsess_to_index(default_session_data)
-    # jc.text_index() not sure what broke here.
+    # this command line tool appears currently broken - or at least not working here.
+    # jc.text_index()
diff --git a/tools/jbrowse2/jbrowse2.xml b/tools/jbrowse2/jbrowse2.xml
index 027617fda0..308a3cf7a3 100644
--- a/tools/jbrowse2/jbrowse2.xml
+++ b/tools/jbrowse2/jbrowse2.xml
@@ -16,12 +16,13 @@
         <include path="jb2_webserver.py"/>
         <include path="jbrowse2.py"/>
         <include path="maf2bed.py"/>
+        <include path="bedscoreplugin.js"/>
     </required_files>
     <version_command>python '${__tool_directory__}/jbrowse2.py' --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
 mkdir -p '$output.files_path' &&
 cp '$trackxml' '$output.files_path/galaxy.xml' &&
-export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 &&
+export JBROWSE2_PATH=\$(realpath \$(dirname \$(which jbrowse))/../opt/jbrowse2) &&
 #if $jbgen.ucol.formcoll=="collect":
     python '$__tool_directory__/autogenJB2.py'
     #for $key in $autoCollection.keys():
@@ -1127,6 +1128,45 @@ export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 &&
                     </has_archive_member>
                 </assert_contents>
             </output>
+        </test> 
+        <test>
+            <repeat name="assemblies">
+                <conditional name="reference_genome">
+                    <param name="genome_type_select" value="history"/>
+                    <param name="genome" value="merlin.fa"/>
+                    <param name="genome.ext" value="fasta"/>
+                    <param name="genome.name" value="Merlin"/>
+                </conditional>
+                <repeat name="track_groups">
+                    <param name="category" value="Default"/>
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="bigwig"/>
+                            <conditional name="useuri">
+                                <param name="annotation" value="bw/m:e.r.l .i-n.bw"/>
+                                <param name="insource" value="history"/>
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                </repeat>
+            </repeat>
+            <section name="jbgen">
+                <param name="zipOut" value="true"/>
+            </section>
+            <output name="output">
+                <assert_contents>
+                    <has_archive_member path="config.json">
+                        <has_text text="QuantitativeTrack"/>
+                        <has_text text="trackId"/>
+                        <has_text text="me.r.l.i-n.bw_0"/>
+                        <has_text text="name"/>
+                        <has_text text="Default"/>
+                        <has_text text="name"/>
+                        <has_text text="assemblyName"/>
+                        <has_text text="merlin.fa"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[
diff --git a/tools/jbrowse2/macros.xml b/tools/jbrowse2/macros.xml
index 6300e4ad5d..b6bac60a6d 100644
--- a/tools/jbrowse2/macros.xml
+++ b/tools/jbrowse2/macros.xml
@@ -25,7 +25,7 @@
         </requirements>
     </xml>
     <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <xml name="creators">
         <creator>
             <person givenName="Helena" familyName="Rasche" url="https://github.com/hexylena"/>
diff --git a/tools/jbrowse2/test-data/bw/m:e.r.l .i-n.bw b/tools/jbrowse2/test-data/bw/m:e.r.l .i-n.bw
new file mode 100755
index 0000000000..ca01be4dad
Binary files /dev/null and b/tools/jbrowse2/test-data/bw/m:e.r.l .i-n.bw differ