From 77b29880c8e9eddaf282e8738542aa57a189f6d2 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 14 Mar 2017 14:45:29 -0400
Subject: [PATCH 1/4] Fix run_tests.sh --dockerize for Mac OS X usage.

Without this I get the error message below and the tests do not execute.

```
./run_tests.sh: line 279: UID: readonly variable
```

This was likely broken with b75ee68d9f6305646a55d816fb1173210e36eab9.
---
 run_tests.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/run_tests.sh b/run_tests.sh
index 69f9c8d95b8..814e2864cb2 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -276,8 +276,8 @@ then
        DOCKER_RUN_EXTRA_ARGS="-v ${tmp}:/tmp ${DOCKER_RUN_EXTRA_ARGS}"
        shift
     fi
-    UID=$(id -u)
-    DOCKER_RUN_EXTRA_ARGS="-e GALAXY_TEST_UID=${UID} ${DOCKER_RUN_EXTRA_ARGS}"
+    MY_UID=$(id -u)
+    DOCKER_RUN_EXTRA_ARGS="-e GALAXY_TEST_UID=${MY_UID} ${DOCKER_RUN_EXTRA_ARGS}"
     echo "Launching docker container for testing..."
     docker $DOCKER_EXTRA_ARGS run $DOCKER_RUN_EXTRA_ARGS -e "BUILD_NUMBER=$BUILD_NUMBER" -e "GALAXY_TEST_DATABASE_TYPE=$db_type" --rm -v `pwd`:/galaxy $DOCKER_IMAGE "$@"
     exit $?

From d1eab2685f652f0b6f8c8119c51acf080c54556e Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 14 Mar 2017 16:26:18 -0400
Subject: [PATCH 2/4] Provide a fallback for GALAXY_TEST_UID if manually
 running Docker tests.

---
 test/docker/base/run_test_wrapper.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/test/docker/base/run_test_wrapper.sh b/test/docker/base/run_test_wrapper.sh
index 54f963882d3..3c7e2adf37b 100644
--- a/test/docker/base/run_test_wrapper.sh
+++ b/test/docker/base/run_test_wrapper.sh
@@ -4,6 +4,8 @@ set -e
 echo "Deleting galaxy user - it may not exist and this is fine."
 deluser galaxy | true
 
+GALAXY_TEST_UID=${GALAXY_TEST_UID:-"1"}
+
 echo "Creating galaxy group with gid $GALAXY_TEST_UID - it may already exist and this is fine."
 groupadd -r galaxy -g "$GALAXY_TEST_UID" | true
 echo "Creating galaxy user with uid $GALAXY_TEST_UID - it may already exist and this is fine."

From d6654838f361a1e3064619cb059f9137579dc376 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 14 Mar 2017 16:26:53 -0400
Subject: [PATCH 3/4] Fix pip install cache inside Galaxy testing container.

It is causing Jenkins to fail throughout on https://github.com/galaxyproject/galaxy/pull/3179.
---
 test/docker/base/run_test_wrapper.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/test/docker/base/run_test_wrapper.sh b/test/docker/base/run_test_wrapper.sh
index 3c7e2adf37b..c2e544f4349 100644
--- a/test/docker/base/run_test_wrapper.sh
+++ b/test/docker/base/run_test_wrapper.sh
@@ -50,10 +50,11 @@ export TOOL_SHED_CONFIG_OVERRIDE_DATABASE_CONNECTION
 
 : ${GALAXY_VIRTUAL_ENV:=.venv}
 
+HOME=/galaxy
 sudo -E -u "#${GALAXY_TEST_UID}" ./scripts/common_startup.sh || { echo "common_startup.sh failed"; exit 1; }
 
 dev_requirements=./lib/galaxy/dependencies/dev-requirements.txt
-[ -f $dev_requirements ] && $GALAXY_VIRTUAL_ENV/bin/pip install -r $dev_requirements
+[ -f $dev_requirements ] && sudo -E -u "#${GALAXY_TEST_UID}" $GALAXY_VIRTUAL_ENV/bin/pip install -r $dev_requirements
 
 echo "Upgrading test database..."
 sudo -E -u "#${GALAXY_TEST_UID}" sh manage_db.sh upgrade

From b1f12d41f66c2b07929c037363fc6d94b890b283 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 20 Mar 2017 09:12:33 -0400
Subject: [PATCH 4/4] Simplify run_test_wrapper.sh per @natefoo comments.

https://github.com/galaxyproject/galaxy/pull/3755/files#r106182107
---
 test/docker/base/run_test_wrapper.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/docker/base/run_test_wrapper.sh b/test/docker/base/run_test_wrapper.sh
index c2e544f4349..7f1b9b70336 100644
--- a/test/docker/base/run_test_wrapper.sh
+++ b/test/docker/base/run_test_wrapper.sh
@@ -4,7 +4,7 @@ set -e
 echo "Deleting galaxy user - it may not exist and this is fine."
 deluser galaxy | true
 
-GALAXY_TEST_UID=${GALAXY_TEST_UID:-"1"}
+: ${GALAXY_TEST_UID:-"1"}
 
 echo "Creating galaxy group with gid $GALAXY_TEST_UID - it may already exist and this is fine."
 groupadd -r galaxy -g "$GALAXY_TEST_UID" | true
@@ -14,7 +14,7 @@ echo "Setting galaxy user password - the operation may fail."
 echo "galaxy:galaxy" | chpasswd | true
 chown -R "$GALAXY_TEST_UID:$GALAXY_TEST_UID" /galaxy_venv
 
-GALAXY_TEST_DATABASE_TYPE=${GALAXY_TEST_DATABASE_TYPE:-"postgres"}
+: ${GALAXY_TEST_DATABASE_TYPE:-"postgres"}
 if [ "$GALAXY_TEST_DATABASE_TYPE" = "postgres" ];
 then
     su -c '/usr/lib/postgresql/9.3/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres