From 134c985f90a538eef623e6bc58c540228658d599 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 19 Sep 2015 13:26:27 +0100
Subject: [PATCH] Updates and fixes for dockerized Galaxy testing.

---
 run_tests.sh                |  2 +-
 test/docker/README.md       | 10 +++++++---
 test/docker/base/Dockerfile | 10 ++++++++++
 3 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/run_tests.sh b/run_tests.sh
index 595777eda0e..14b38ad0dc5 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -91,7 +91,7 @@ then
     fi
     DOCKER_EXTRA_ARGS=${DOCKER_ARGS:-""}
     DOCKER_RUN_EXTRA_ARGS=${DOCKER_ARGS:-""}
-    DOCKER_IMAGE=${DOCKER_IMAGE:-"galaxyprojectdotorg/testing-base"}
+    DOCKER_IMAGE=${DOCKER_IMAGE:-"galaxy/testing-base"}
     docker $DOCKER_EXTRA_ARGS run $DOCKER_RUN_EXTRA_ARGS -e "GALAXY_TEST_DATABASE_TYPE=$db_type" --rm -v `pwd`:/galaxy $DOCKER_IMAGE "$@"
     exit $?
 fi
diff --git a/test/docker/README.md b/test/docker/README.md
index 14a86fc9e4c..ed9bd8cbf7a 100644
--- a/test/docker/README.md
+++ b/test/docker/README.md
@@ -1,9 +1,13 @@
 Setup Docker environment for use with testing using the following
-commands (until this is on Docker hub).
+commands.
 
     % cd test/base
-    % docker build -t galaxyprojectdotorg/testing-base .
+    % docker build -t galaxy/testing-base .
 
-This will create a docker container ready to run most of Galaxy tests
+Alternatively, this can be fetched from [Dockerhub](https://hub.docker.com/).
+
+    % docker pull galaxy/testing-base
+
+The resulting docker container is ready to run most of Galaxy tests
 (functional tests for specific bioinformatics tools may still fail for
 now until they are migrated out of Galaxy and to the tool shed).
diff --git a/test/docker/base/Dockerfile b/test/docker/base/Dockerfile
index 2b9df242a04..1a735a169f0 100644
--- a/test/docker/base/Dockerfile
+++ b/test/docker/base/Dockerfile
@@ -62,6 +62,16 @@ RUN cd $GALAXY_ROOT && \
     sh /opt/galaxy/start_mysql.sh && \
     GALAXY_CONFIG_DATABASE_CONNECTION="mysql://galaxy:galaxy@localhost/galaxy?unix_socket=/var/run/mysqld/mysqld.sock" sh create_db.sh
 
+# bcftools for Galaxy.
+RUN mkdir -p /tmp/install && \
+    cd /tmp/install && \
+    wget https://github.com/samtools/bcftools/releases/download/1.2/bcftools-1.2.tar.bz2 && \
+    tar xvjf bcftools-1.2.tar.bz2 && \
+    cd bcftools-1.2 && \
+    make && \
+    make install && \
+    cd && rm -rf /tmp/install
+    
 ADD run_test_wrapper.sh /usr/local/bin/run_test_wrapper.sh
 EXPOSE :8080
 EXPOSE :80