Merge pull request #759 from jmchilton/dockerize_test

Updates and fixes for dockerized Galaxy testing.

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

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).

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