diff --git a/tools/jbrowse2/jbrowse2.py b/tools/jbrowse2/jbrowse2.py
index 24188ca42b..b8a0024a4b 100644
--- a/tools/jbrowse2/jbrowse2.py
+++ b/tools/jbrowse2/jbrowse2.py
@@ -411,7 +411,7 @@ def __init__(self, outdir, jbrowse2path):
             []
         )  # for default session - these are read as first line of the assembly .fai
         self.giURL = GALAXY_INFRASTRUCTURE_URL
-        self.outdir = outdir
+        self.outdir = os.path.abspath(outdir)
         self.jbrowse2path = jbrowse2path
         os.makedirs(self.outdir, exist_ok=True)
         self.genome_names = []
@@ -444,7 +444,7 @@ def subprocess_popen(self, command, cwd=True):
             log.debug(command)
         p = subprocess.Popen(
             command,
-            cwd=self.get_cwd(cwd),
+            cwd=self.outdir,
             shell=True,
             stdin=subprocess.PIPE,
             stdout=subprocess.PIPE,
@@ -1440,8 +1440,6 @@ def add_default_session(self, default_data):
                 )
             session_views.append(view_json)
         session_name = default_data.get("session_name", "New session")
-        for key, value in mapped_chars.items():
-            session_name = session_name.replace(value, key)
         session_json["name"] = session_name
 
         if "views" not in session_json:
diff --git a/tools/jbrowse2/jbrowse2.xml b/tools/jbrowse2/jbrowse2.xml
index 5b863f1204..027617fda0 100644
--- a/tools/jbrowse2/jbrowse2.xml
+++ b/tools/jbrowse2/jbrowse2.xml
@@ -639,13 +639,10 @@ export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 &&
                 <param name="zipOut" value="true"/>
                 <param name="session_name" value="New test session"/>
             </section>
-            <!-- use the following line to generate a ZIP file to inspect it -->
-            <!--output name="output" file="jbrowse2_result02.zip" ftype="zip" compare="sim_size"-->
             <output name="output" ftype="zip">
                 <assert_contents>
-                    <has_archive_member path=".*" n="637" delta="10"/>
+                    <has_archive_member path=".*" n="678" delta="10"/>
                     <has_archive_member path="index.html"/>
-                    <has_archive_member path="static/media/roboto-latin-400-normal.3f2b9a42f643e62a49b7.woff"/>
                     <has_archive_member path="manifest.json">
                         <has_text text="favicon.ico"/>
                         <has_text text="background_color"/>
@@ -697,13 +694,10 @@ export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 &&
                 <param name="session_name" value="Collection test"/>
                 <param name="ucol|formcoll" value="collect"/>
             </section>
-            <!-- use the following line to generate a ZIP file to inspect it -->
-            <!--output name="output" file="jbrowse2_result01.zip" ftype="zip" compare="sim_size"-->
             <output name="output" ftype="zip">
                 <assert_contents>
-                    <has_archive_member path=".*" n="611" delta="10"/>
+                    <has_archive_member path=".*" n="652" delta="10"/>
                     <has_archive_member path="index.html"/>
-                    <has_archive_member path="static/media/roboto-latin-400-normal.3f2b9a42f643e62a49b7.woff"/>
                     <has_archive_member path="manifest.json">
                         <has_text text="favicon.ico"/>
                         <has_text text="background_color"/>
@@ -1119,10 +1113,8 @@ export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 &&
             </section>
             <output name="output" ftype="zip">
                 <assert_contents>
-                    <!-- roughly 590 files in an archive -->
-                    <has_archive_member path=".*" n="608" delta="30"/>
+                    <has_archive_member path=".*" n="649" delta="30"/>
                     <has_archive_member path="index.html"/>
-                    <has_archive_member path="static/media/roboto-latin-400-normal.3f2b9a42f643e62a49b7.woff"/>
                     <has_archive_member path="manifest.json">
                         <has_text text="favicon.ico"/>
                         <has_text text="background_color"/>
diff --git a/tools/jbrowse2/macros.xml b/tools/jbrowse2/macros.xml
index a8e4f962a9..6300e4ad5d 100644
--- a/tools/jbrowse2/macros.xml
+++ b/tools/jbrowse2/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.13.1</token>
+    <token name="@TOOL_VERSION@">2.15.4</token>
     <xml name="edamInc">
         <edam_topics>
             <edam_topic>topic_3307</edam_topic>
@@ -15,17 +15,17 @@
             <requirement type="package" version="@TOOL_VERSION@">jbrowse2</requirement>
             <requirement type="package" version="1.82">biopython</requirement>
             <requirement type="package" version="0.7.1">bcbio-gff</requirement>
-            <requirement type="package" version="1.19">samtools</requirement>
+            <requirement type="package" version="1.21">samtools</requirement>
             <requirement type="package" version="6.0.1">pyyaml</requirement>
             <requirement type="package" version="1.11">tabix</requirement>
             <requirement type="package" version="4.6.0">findutils</requirement>
-            <requirement type="package" version="0.0.12-0">hictk</requirement>
+            <requirement type="package" version="1.0.0">hictk</requirement>
             <requirement type="package" version="3.0">zip</requirement>
             <yield/>
         </requirements>
     </xml>
     <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="creators">
         <creator>
             <person givenName="Helena" familyName="Rasche" url="https://github.com/hexylena"/>