From 1f69bf32e8cf3c073804d2cdbb3823e14f1a8ce5 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@tgac.ac.uk>
Date: Thu, 18 Aug 2016 14:03:59 +0100
Subject: [PATCH 1/2] Fix run.sh --daemon

Broken in commit d5c52cadfd0007338d4c89f505ff272e9acae9f9 .
Partial backport from #2765 .
Close #2724.
---
 run.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/run.sh b/run.sh
index 901d7e46172..bd81956684f 100755
--- a/run.sh
+++ b/run.sh
@@ -34,7 +34,7 @@ do
             shift
             ;;
         --daemon|--restart|restart)
-            if [ "$1"=="--restart" ]
+            if [ "$1" == "--restart" ]
             then
                 paster_args="$paster_args restart"
             else

From a134587c893f6afa6f8bab1e9df7ff4ef74fa29c Mon Sep 17 00:00:00 2001
From: Dave Bouvier <dave@bx.psu.edu>
Date: Fri, 8 Apr 2016 14:42:20 -0400
Subject: [PATCH 2/2] Correctly check set_environment declarations when
 updating repository.

---
 lib/tool_shed/util/shed_util_common.py | 22 +++++++++++++++-------
 1 file changed, 15 insertions(+), 7 deletions(-)

diff --git a/lib/tool_shed/util/shed_util_common.py b/lib/tool_shed/util/shed_util_common.py
index 51467fc6ed0..cc70003a177 100644
--- a/lib/tool_shed/util/shed_util_common.py
+++ b/lib/tool_shed/util/shed_util_common.py
@@ -98,7 +98,7 @@ def can_eliminate_repository_dependency(metadata_dict, tool_shed_url, name, owne
     return True
 
 
-def can_eliminate_tool_dependency(metadata_dict, name, type, version):
+def can_eliminate_tool_dependency(metadata_dict, name, dependency_type, version):
     """
     Determine if the relationship between a tool_dependency record
     associated with a tool_shed_repository record on the Galaxy side
@@ -106,12 +106,20 @@ def can_eliminate_tool_dependency(metadata_dict, name, type, version):
     """
     td_dict = metadata_dict.get('tool_dependencies', {})
     for td_key, td_val in td_dict.items():
-        n = td_val.get('name', None)
-        t = td_val.get('type', None)
-        v = td_val.get('version', None)
-        if n == name and t == type and v == version:
-            # The tool dependency is current, so keep it.
-            return False
+        if td_key == 'set_environment':
+            for td in td_val:
+                n = td.get('name', None)
+                t = td.get('type', None)
+                if n == name and t == dependency_type:
+                    # The tool dependency is current, so keep it.
+                    return False
+        else:
+            n = td_val.get('name', None)
+            t = td_val.get('type', None)
+            v = td_val.get('version', None)
+            if n == name and t == dependency_type and v == version:
+                # The tool dependency is current, so keep it.
+                return False
     return True