diff --git a/config/plugins/interactive_environments/cellxgene/config/allowed_images.yml.sample b/config/plugins/interactive_environments/cellxgene/config/allowed_images.yml.sample
index f3ec2cde2b8..2a4edc35be7 100644
--- a/config/plugins/interactive_environments/cellxgene/config/allowed_images.yml.sample
+++ b/config/plugins/interactive_environments/cellxgene/config/allowed_images.yml.sample
@@ -1,5 +1,5 @@
 ---
 -
-    image: quay.io/galaxy/cellxgene-galaxy-ie:2019.01.30
+    image: quay.io/galaxy/cellxgene-galaxy-ie:2019.05.13
     description: |
         An interactive data explorer for single-cell transcriptomics datasets
diff --git a/config/plugins/interactive_environments/cellxgene/docker/Dockerfile b/config/plugins/interactive_environments/cellxgene/docker/Dockerfile
index 1d7295f01bd..cd842996fb9 100644
--- a/config/plugins/interactive_environments/cellxgene/docker/Dockerfile
+++ b/config/plugins/interactive_environments/cellxgene/docker/Dockerfile
@@ -1,9 +1,13 @@
 FROM python:3.6.8-slim
+
+RUN apt-get update && apt-get install -y \
+    net-tools \
+ && rm -rf /var/lib/apt/lists/*
  
-RUN pip3 install cellxgene scanpy==1.4 && rm -rf ~/.cache
+RUN pip3 install cellxgene galaxy-ie-helpers && rm -rf ~/.cache
 
 ADD ./run_cellxgene.sh /
 
-##ENTRYPOINT ["/run_cellxgene.sh"]
+ENTRYPOINT ["/run_cellxgene.sh"]
 
 EXPOSE 80
diff --git a/config/plugins/interactive_environments/cellxgene/docker/run_cellxgene.sh b/config/plugins/interactive_environments/cellxgene/docker/run_cellxgene.sh
index cb9413d7bc7..30fd71b2e05 100755
--- a/config/plugins/interactive_environments/cellxgene/docker/run_cellxgene.sh
+++ b/config/plugins/interactive_environments/cellxgene/docker/run_cellxgene.sh
@@ -1,3 +1,5 @@
 #!/bin/sh
 
-cellxgene launch --host 0.0.0.0 --port 8080 /tmp/galaxy_cellxgene*
+get -i ${DATASET_HID} \
+    && mv /import/${DATASET_HID} /import/${DATASET_HID}.h5ad \
+    && cellxgene launch --host 0.0.0.0 --port 80 /import/${DATASET_HID}.h5ad
diff --git a/config/plugins/interactive_environments/cellxgene/templates/cellxgene.mako b/config/plugins/interactive_environments/cellxgene/templates/cellxgene.mako
index 8651f5b50af..1965844f09c 100644
--- a/config/plugins/interactive_environments/cellxgene/templates/cellxgene.mako
+++ b/config/plugins/interactive_environments/cellxgene/templates/cellxgene.mako
@@ -2,12 +2,11 @@
 <%
     ie_request.load_deploy_config()
 
-    # Make the dataset available inside the container
-    data_file = ie_request.volume('/input/file.' + hda.ext, hda.file_name, mode='ro')
-
     ie_request.launch(
-       image = trans.request.params.get('image_tag', None),
-       volumes = [data_file]
+        image = trans.request.params.get('image_tag', None),
+        env_override={
+            'dataset_hid': hda.hid
+        }
     )
 
     url = ie_request.url_template('${PROXY_URL}')
diff --git a/lib/galaxy/jobs/output_checker.py b/lib/galaxy/jobs/output_checker.py
index a5fb26ba0e5..0d4bae30de6 100644
--- a/lib/galaxy/jobs/output_checker.py
+++ b/lib/galaxy/jobs/output_checker.py
@@ -146,10 +146,12 @@ def check_output(stdio_regexes, stdio_exit_codes, stdout, stderr, tool_exit_code
             if stderr:
                 state = DETECTED_JOB_STATE.GENERIC_ERROR
 
-        if DETECTED_JOB_STATE != DETECTED_JOB_STATE.OK and stderr:
+        if state != DETECTED_JOB_STATE.OK and stderr:
             if stderr:
                 peak = stderr[0:ERROR_PEAK]
-                log.debug("job failed, standard error is - [%s]" % peak)
+            else:
+                peak = ""
+            log.debug("job failed, detected state %s, standard error is - [%s]" % (state, peak))
     except Exception:
         log.exception("Job state check encountered unexpected exception; assuming execution successful")
 
diff --git a/test/functional/tools/realtimetool_cellxgene.xml b/test/functional/tools/realtimetool_cellxgene.xml
index 67c08ce118b..6431479dbe6 100644
--- a/test/functional/tools/realtimetool_cellxgene.xml
+++ b/test/functional/tools/realtimetool_cellxgene.xml
@@ -4,12 +4,14 @@
     </requirements>
     <realtime>
         <entry_point name="cellxgene_single_cell_visualisation">
-            <port>8080</port>
+            <port>80</port>
         </entry_point>
     </realtime>
-    <command>
-        cp '$input' /tmp/galaxy_cellxgene_${input.element_identifier}.h5ad;
-        /run_cellxgene.sh
+    <command><![CDATA[
+        cp '${inpu}' '/tmp/galaxy_cellxgene_${input.element_identifier}.h5ad'
+        &&
+        cellxgene launch --host 0.0.0.0 --port 80 /tmp/galaxy_cellxgene*
+    ]]>
     </command>
     <inputs>
         <param name="input" type="data" format="h5ad" label="Concatenate Dataset"/>