From 2210f83da95b702ea10f7809b29ee77d54fc1529 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 5 Oct 2015 14:18:41 +0100
Subject: [PATCH 1/2] Remove run_functional_tests.sh.

It has been deprecated who a while and removed once already - hopefully now we can kill it.
---
 run_functional_tests.sh | 1 -
 1 file changed, 1 deletion(-)
 delete mode 120000 run_functional_tests.sh

diff --git a/run_functional_tests.sh b/run_functional_tests.sh
deleted file mode 120000
index 5236e32d82f..00000000000
--- a/run_functional_tests.sh
+++ /dev/null
@@ -1 +0,0 @@
-run_tests.sh
\ No newline at end of file

From 596f9116f25f384899f9c7acb5517d57b88ca358 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 5 Oct 2015 14:19:27 +0100
Subject: [PATCH 2/2] Use framework test tools for --api and --casperjs tests.

These tests are explicitly designed to test the framework and use a tool panel. ``sh run_tests.sh`` and ``sh run_tests.sh -id`` are meant to test Galaxy's configuration to some degree, and other tests qunit, unit, and toolshed do not depend on the toolbox.
---
 run_tests.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/run_tests.sh b/run_tests.sh
index cce3eae0a62..da27d80adac 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -126,6 +126,7 @@ do
           fi 
           ;;
     -a|-api|--api)
+          with_framework_test_tools_arg="-with_framework_test_tools"
           test_script="./scripts/functional_tests.py"
           report_file="./run_api_tests.html"
           if [ $# -gt 1 ]; then
@@ -173,6 +174,7 @@ do
       -j|-casperjs|--casperjs)
           # TODO: Support running casper tests against existing
           # Galaxy instances.
+          with_framework_test_tools_arg="-with_framework_test_tools"
           if [ $# -gt 1 ]; then
               casperjs_test_name=$2
               shift 2