diff --git a/test/integration/embedded_pulsar_job_conf.xml b/test/integration/embedded_pulsar_job_conf.xml
deleted file mode 100644
index 54b204ec8075..000000000000
--- a/test/integration/embedded_pulsar_job_conf.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0"?>
-<!-- A job config for testing the Pulsar embedded runner -->
-<job_conf>
-    <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
-        <plugin id="pulsar_embed" type="runner" load="galaxy.jobs.runners.pulsar:PulsarEmbeddedJobRunner">
-        </plugin>
-    </plugins>
-    <destinations default="pulsar_embed">
-        <destination id="local" runner="local">
-        </destination>
-        <destination id="pulsar_embed" runner="pulsar_embed">
-            <param id="remote_metadata">true</param>
-        </destination>
-    </destinations>
-    <tools>
-        <tool class="local" destination="local" />
-    </tools>
-</job_conf>
diff --git a/test/integration/embedded_pulsar_job_conf.yml b/test/integration/embedded_pulsar_job_conf.yml
new file mode 100644
index 000000000000..ec67df2c4770
--- /dev/null
+++ b/test/integration/embedded_pulsar_job_conf.yml
@@ -0,0 +1,22 @@
+runners:
+  local:
+    load: galaxy.jobs.runners.local:LocalJobRunner
+  pulsar_embed:
+    load: galaxy.jobs.runners.pulsar:PulsarEmbeddedJobRunner
+    pulsar_app_config:  # this doesn't start without disabling - filelock problem
+      tool_dependency_dir: none
+      conda_auto_init: false
+      conda_auto_install: false
+
+execution:
+  default: pulsar_embed
+  environments:
+    local:
+      runner: local
+    pulsar_embed:
+      runner: pulsar_embed
+      remote_metadata: true
+
+tools:
+- class: local
+  environment: local
diff --git a/test/integration/embedded_pulsar_metadata_extended_job_conf.yml b/test/integration/embedded_pulsar_metadata_extended_job_conf.yml
index aeab99c5454b..7912f53941eb 100644
--- a/test/integration/embedded_pulsar_metadata_extended_job_conf.yml
+++ b/test/integration/embedded_pulsar_metadata_extended_job_conf.yml
@@ -3,6 +3,10 @@ runners:
     load: galaxy.jobs.runners.local:LocalJobRunner
   pulsar_embed:
     load: galaxy.jobs.runners.pulsar:PulsarEmbeddedJobRunner
+    pulsar_app_config:
+      tool_dependency_dir: none
+      conda_auto_init: false
+      conda_auto_install: false
 
 execution:
   default: pulsar_embed
diff --git a/test/integration/test_job_environments.py b/test/integration/test_job_environments.py
index c32320f7d625..1de561d8239c 100644
--- a/test/integration/test_job_environments.py
+++ b/test/integration/test_job_environments.py
@@ -15,7 +15,7 @@
 IO_INJECTION_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "io_injection_job_conf.yml")
 SETS_TMP_DIR_TO_TRUE_JOB_CONFIG = os.path.join(SCRIPT_DIRECTORY, "sets_tmp_dir_to_true_job_conf.xml")
 SETS_TMP_DIR_AS_EXPRESSION_JOB_CONFIG = os.path.join(SCRIPT_DIRECTORY, "sets_tmp_dir_expression_job_conf.xml")
-EMBEDDED_PULSAR_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "embedded_pulsar_job_conf.xml")
+EMBEDDED_PULSAR_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "embedded_pulsar_job_conf.yml")
 
 JobEnvironmentProperties = collections.namedtuple(
     "JobEnvironmentProperties",
diff --git a/test/integration/test_pulsar_embedded.py b/test/integration/test_pulsar_embedded.py
index a949a8a8f5e4..c2d37c265273 100644
--- a/test/integration/test_pulsar_embedded.py
+++ b/test/integration/test_pulsar_embedded.py
@@ -5,7 +5,7 @@
 from galaxy_test.driver import integration_util
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
-EMBEDDED_PULSAR_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "embedded_pulsar_job_conf.xml")
+EMBEDDED_PULSAR_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "embedded_pulsar_job_conf.yml")
 
 
 class EmbeddedPulsarIntegrationInstance(integration_util.IntegrationInstance):