diff --git a/client/galaxy/scripts/mvc/tool/tool-form-composite.js b/client/galaxy/scripts/mvc/tool/tool-form-composite.js
index 9a6cd1ab24e..1beea452ce9 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form-composite.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form-composite.js
@@ -119,7 +119,7 @@ var View = Backbone.View.extend({
                         input.help = input.step_linked ? `${input.help}, ` : "";
                         input.help += `Output dataset '${connection.output_name}' from step ${parseInt(i) + 1}`;
                         input.step_linked = input.step_linked || [];
-                        input.step_linked.push(step);
+                        input.step_linked.push({ index: step.index, step_type: step.step_type });
                     }
                 });
             });
@@ -314,31 +314,34 @@ var View = Backbone.View.extend({
 
     /** Render job caching option */
     _renderUseCachedJob: function() {
-       var extra_user_preferences = {};
-       if (Galaxy.user.attributes.preferences && 'extra_user_preferences' in Galaxy.user.attributes.preferences){
-           extra_user_preferences = JSON.parse(Galaxy.user.attributes.preferences.extra_user_preferences);
-       }
-       var display_use_cached_job_checkbox = 'use_cached_job|use_cached_job_checkbox' in extra_user_preferences ? extra_user_preferences['use_cached_job|use_cached_job_checkbox'] : false ;
-       this.display_use_cached_job_checkbox = display_use_cached_job_checkbox === 'true';
-       if (this.display_use_cached_job_checkbox){
+        var extra_user_preferences = {};
+        if (Galaxy.user.attributes.preferences && "extra_user_preferences" in Galaxy.user.attributes.preferences) {
+            extra_user_preferences = JSON.parse(Galaxy.user.attributes.preferences.extra_user_preferences);
+        }
+        var display_use_cached_job_checkbox =
+            "use_cached_job|use_cached_job_checkbox" in extra_user_preferences
+                ? extra_user_preferences["use_cached_job|use_cached_job_checkbox"]
+                : false;
+        this.display_use_cached_job_checkbox = display_use_cached_job_checkbox === "true";
+        if (this.display_use_cached_job_checkbox) {
             this.job_options_form = new Form({
                 cls: "ui-portlet-narrow",
                 title: "<b>Job re-use Options</b>",
                 inputs: [
-                            {
-                                type: "conditional",
-                                name: "use_cached_job",
-                                test_param: {
-                                    name: "check",
-                                    label: "BETA: Attempt to reuse jobs with identical parameters?",
-                                    type: "boolean",
-                                    value: "false",
-                                    help: "This may skip executing jobs that you have already run."
-                                },
-                            }
-                        ]
-           });
-           this._append(this.$steps, this.job_options_form.$el);
+                    {
+                        type: "conditional",
+                        name: "use_cached_job",
+                        test_param: {
+                            name: "check",
+                            label: "BETA: Attempt to reuse jobs with identical parameters?",
+                            type: "boolean",
+                            value: "false",
+                            help: "This may skip executing jobs that you have already run."
+                        }
+                    }
+                ]
+            });
+            this._append(this.$steps, this.job_options_form.$el);
         }
     },
 
@@ -542,8 +545,8 @@ var View = Backbone.View.extend({
             batch: true
         };
         if (this.display_use_cached_job_checkbox) {
-            job_def['use_cached_job'] = this.job_options_form.data.create()["use_cached_job|check"] === 'true';
-	}
+            job_def["use_cached_job"] = this.job_options_form.data.create()["use_cached_job|check"] === "true";
+        }
         var validated = true;
         for (var i in this.forms) {
             var form = this.forms[i];
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-node.js b/client/galaxy/scripts/mvc/workflow/workflow-node.js
index e32591b7373..67a10df10a3 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-node.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-node.js
@@ -179,13 +179,19 @@ var Node = Backbone.Model.extend({
         // Remove active class
         $(element).removeClass("toolForm-active");
     },
+    set_tool_version: function() {
+        if (this.config_form) {
+            this.tool_version = this.config_form.version;
+            this.content_id = this.config_form.id;
+        }
+    },
     init_field_data: function(data) {
         if (data.type) {
             this.type = data.type;
         }
         this.name = data.name;
         this.config_form = data.config_form;
-        this.tool_version = this.config_form && this.config_form.version;
+        this.set_tool_version();
         this.tool_state = data.tool_state;
         this.errors = data.errors;
         this.tooltip = data.tooltip ? data.tooltip : "";
@@ -263,7 +269,7 @@ var Node = Backbone.Model.extend({
         });
         this.tool_state = data.tool_state;
         this.config_form = data.config_form;
-        this.tool_version = this.config_form && this.config_form.version;
+        this.set_tool_version();
         this.errors = data.errors;
         this.annotation = data.annotation;
         this.label = data.label;
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index daefe7a7e97..2b7325a2ed6 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -327,27 +327,35 @@ class Bam(Binary):
 
     def get_chunk(self, trans, dataset, offset=0, ck_size=None):
         index_file = dataset.metadata.bam_index
-        with pysam.AlignmentFile(dataset.file_name, "rb", index_filename=index_file.file_name) as bamfile:
-            ck_size = 300  # 300 lines
-            ck_data = ""
-            header_line_count = 0
-            if offset == 0:
-                ck_data = bamfile.text.replace('\t', ' ')
-                header_line_count = bamfile.text.count('\n')
-            else:
-                bamfile.seek(offset)
-            for line_number, alignment in enumerate(bamfile) :
-                # return only Header lines if 'header_line_count' exceeds 'ck_size'
-                # FIXME: Can be problematic if bam has million lines of header
-                offset = bamfile.tell()
-                if (line_number + header_line_count) > ck_size:
-                    break
-                else:
-                    bamline = alignment.tostring(bamfile)
-                    # Galaxy display each tag as separate column because 'tostring()' funcition put tabs in between each tag of tags column.
-                    # Below code will remove spaces between each tag.
-                    bamline_modified = ('\t').join(bamline.split()[:11] + [(' ').join(bamline.split()[11:])])
-                    ck_data = "%s\n%s" % (ck_data, bamline_modified)
+        if not offset == -1:
+            try:
+                with pysam.AlignmentFile(dataset.file_name, "rb", index_filename=index_file.file_name) as bamfile:
+                    ck_size = 300  # 300 lines
+                    ck_data = ""
+                    header_line_count = 0
+                    if offset == 0:
+                        ck_data = bamfile.text.replace('\t', ' ')
+                        header_line_count = bamfile.text.count('\n')
+                    else:
+                        bamfile.seek(offset)
+                    for line_number, alignment in enumerate(bamfile) :
+                        # return only Header lines if 'header_line_count' exceeds 'ck_size'
+                        # FIXME: Can be problematic if bam has million lines of header
+                        offset = bamfile.tell()
+                        if (line_number + header_line_count) > ck_size:
+                            break
+                        else:
+                            bamline = alignment.tostring(bamfile)
+                            # Galaxy display each tag as separate column because 'tostring()' funcition put tabs in between each tag of tags column.
+                            # Below code will remove spaces between each tag.
+                            bamline_modified = ('\t').join(bamline.split()[:11] + [(' ').join(bamline.split()[11:])])
+                            ck_data = "%s\n%s" % (ck_data, bamline_modified)
+            except Exception as e:
+                offset = -1
+                ck_data = "Could not display BAM file, error was:\n%s" % e.message
+        else:
+            ck_data = ''
+            offset = -1
         return dumps({'ck_data': util.unicodify(ck_data),
                       'offset': offset})