From c6403acd0f18196c0453a90fe89ccf861d7a28d6 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 20 Jun 2018 15:36:01 -0400
Subject: [PATCH 1/5] Fix logging bug.

---
 lib/galaxy/tools/parameters/output_collect.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tools/parameters/output_collect.py b/lib/galaxy/tools/parameters/output_collect.py
index 4a562e3651a..00fe56383c9 100644
--- a/lib/galaxy/tools/parameters/output_collect.py
+++ b/lib/galaxy/tools/parameters/output_collect.py
@@ -404,7 +404,7 @@ class JobContext(object):
                 dbkey = self.input_dbkey
 
             # Create new primary dataset
-            name = fields_match.name or designation
+            dataset_name = fields_match.name or designation
 
             link_data = discovered_file.match.link_data
 
@@ -413,7 +413,7 @@ class JobContext(object):
                 designation=designation,
                 visible=visible,
                 dbkey=dbkey,
-                name=name,
+                name=dataset_name,
                 filename=filename,
                 metadata_source_name=metadata_source_name,
                 link_data=link_data,

From 572f38d1fb47e914ad10766007c855786e1643a2 Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Thu, 21 Jun 2018 15:44:05 -0400
Subject: [PATCH 2/5] move the sanitization to the try/except block

as it may fail (and it did, on Main)
---
 scripts/grt/export.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/grt/export.py b/scripts/grt/export.py
index 24587d4317b..aa824056e51 100644
--- a/scripts/grt/export.py
+++ b/scripts/grt/export.py
@@ -380,9 +380,9 @@ def main(argv):
             if job_tool_map[param[0]] in blacklisted_tools:
                 continue
 
-            sanitized = san.sanitize_data(job_tool_map[param[0]], param[1], param[2])
-
             try:
+                sanitized = san.sanitize_data(job_tool_map[param[0]], param[1], param[2])
+
                 handle_params.write(str(param[0]))
                 handle_params.write('\t')
                 handle_params.write(param[1])

From 9967639bac92eb3f7103794663f41b88f11baa9c Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 22 Jun 2018 00:19:00 -0400
Subject: [PATCH 3/5] Comma-separate tool names in missing tools error message

---
 lib/galaxy/managers/workflows.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
index 3c280c9ee7f..92c2e679770 100644
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -393,7 +393,7 @@ class WorkflowContentsManager(UsesAnnotations):
                     errors[step.id] = step_errors
         if missing_tools:
             workflow.annotation = self.get_item_annotation_str(trans.sa_session, trans.user, workflow)
-            raise exceptions.MessageException('Following tools missing: %s' % missing_tools)
+            raise exceptions.MessageException('Following tools missing: %s' % ', '.join(missing_tools))
         workflow.annotation = self.get_item_annotation_str(trans.sa_session, trans.user, workflow)
         step_order_indices = {}
         for step in workflow.steps:

From fa2b6baef71984c0559c53ff5750d1fe9b77163e Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 22 Jun 2018 13:22:51 -0400
Subject: [PATCH 4/5] Revert "Remove bam to bai converter"

This reverts commit 7e2727bc0a74868198e7e457f99df3d1e39f1ddb.
---
 config/datatypes_conf.xml.sample               |  1 +
 lib/galaxy/datatypes/converters/bam_to_bai.xml | 14 ++++++++++++++
 2 files changed, 15 insertions(+)
 create mode 100644 lib/galaxy/datatypes/converters/bam_to_bai.xml

diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index 9fea0cc01d9..10b791f9933 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -9,6 +9,7 @@
     <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true" description="blastz pairwise alignment format.  Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines.  Blocks are separated from one another by blank lines.  The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Axt"/>
     <datatype extension="fli" type="galaxy.datatypes.tabular:FeatureLocationIndex" display_in_upload="false"/>
     <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
+      <converter file="bam_to_bai.xml" target_datatype="bai"/>
       <converter file="bam_to_bigwig_converter.xml" target_datatype="bigwig"/>
       <converter file="to_qname_sorted_bam.xml" target_datatype="qname_sorted.bam"/>
       <display file="ucsc/bam.xml" />
diff --git a/lib/galaxy/datatypes/converters/bam_to_bai.xml b/lib/galaxy/datatypes/converters/bam_to_bai.xml
new file mode 100644
index 00000000000..1587ff83cab
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/bam_to_bai.xml
@@ -0,0 +1,14 @@
+<tool id="CONVERTER_Bam_Bai_0" name="Bam to Bai" version="1.0.0" hidden="true">
+    <requirements>
+        <requirement type="package">samtools</requirement>
+    </requirements>
+    <command>samtools index '$input1' '$output1'</command>
+    <inputs>
+        <param format="bam" name="input1" type="data" label="Choose BAM"/>
+    </inputs>
+    <outputs>
+        <data format="bai" name="output1"/>
+    </outputs>
+    <help>
+    </help>
+</tool>

From 5f24794efdad757b77c75c3aa111da7a11c5bb47 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 22 Jun 2018 19:44:24 +0200
Subject: [PATCH 5/5] Add basic .bai datatype

---
 config/datatypes_conf.xml.sample | 1 +
 1 file changed, 1 insertion(+)

diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index 10b791f9933..923d31a249a 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -18,6 +18,7 @@
       <display file="igb/bam.xml" />
       <display file="iobio/bam.xml" />
     </datatype>
+    <datatype extension="bai" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="false"/>
     <datatype extension="qname_input_sorted.bam" type="galaxy.datatypes.binary:BamInputSorted" mimetype="application/octet-stream" display_in_upload="false" description="A binary file compressed in the BGZF format with a '.bam' file extension and sorted based on the aligner output." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
     </datatype>
     <datatype extension="qname_sorted.bam" type="galaxy.datatypes.binary:BamQuerynameSorted" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension and sorted by queryname." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">