diff --git a/test/docker/base/Dockerfile b/test/docker/base/Dockerfile index 4692b0820d3..7b1bf0f0e1e 100644 --- a/test/docker/base/Dockerfile +++ b/test/docker/base/Dockerfile @@ -1,15 +1,16 @@ -FROM toolshed/requirements +FROM ubuntu:16.04 MAINTAINER John Chilton -ENV MYSQL_MAJOR=5.6 -ENV GALAXY_ROOT=/galaxy -ENV GALAXY_VIRTUAL_ENV /galaxy_venv +ENV MYSQL_MAJOR=5.7 \ + POSTGRES_MAJOR=9.5 \ + GALAXY_ROOT=/galaxy \ + GALAXY_VIRTUAL_ENV=/galaxy_venv # Pre-install a bunch of packages to speed up ansible steps. -RUN apt-get update -y && apt-get install -y software-properties-common curl && \ +RUN apt-get update -y && apt-get install -y software-properties-common apt-transport-https curl && \ apt-add-repository -y ppa:ansible/ansible && \ curl -s https://deb.nodesource.com/gpgkey/nodesource.gpg.key | apt-key add - && \ - echo 'deb https://deb.nodesource.com/node trusty main' > /etc/apt/sources.list.d/nodesource.list && \ + curl -sL https://deb.nodesource.com/setup_8.x | bash - && \ apt-key adv --keyserver pool.sks-keyservers.net --recv-keys A4A9406876FCBD3C456770C88C718D3B5072E1F5 && \ echo "deb http://repo.mysql.com/apt/ubuntu/ trusty mysql-${MYSQL_MAJOR}" > /etc/apt/sources.list.d/mysql.list && \ { \ @@ -19,19 +20,25 @@ RUN apt-get update -y && apt-get install -y software-properties-common curl && \ echo mysql-community-server mysql-community-server/remove-test-db select false; \ } | debconf-set-selections && \ apt-get update -y && \ - apt-get install -y libpq-dev postgresql postgresql-client postgresql-plpython-9.3 \ - ansible postgresql-server-dev-9.3 wget mysql-server="${MYSQL_MAJOR}"* libmysqlclient-dev="${MYSQL_MAJOR}"* \ + apt-get install -y libpq-dev postgresql postgresql-client \ + ansible wget mysql-server="${MYSQL_MAJOR}"* libmysqlclient-dev="${MYSQL_MAJOR}"* \ slurm-llnl libmunge-dev slurm-drmaa-dev ant atop axel bioperl cmake curl \ g++ gcc gfortran git-core htop iftop iotop ipython libffi-dev liblapack-dev \ libncurses5-dev libopenblas-dev libpam0g-dev libpq-dev libsparsehash-dev make \ mercurial nginx-extras nmon patch postgresql postgresql \ - postgresql-client postgresql-plpython-9.3 python-boto python-dev \ + postgresql-client python-boto python-dev \ python-prettytable python-psycopg2 python-virtualenv python-pip \ - postgresql-server-dev-9.3 rsync slurm-drmaa-dev swig sysstat unzip \ + rsync slurm-drmaa-dev swig sysstat unzip \ + autoconf automake build-essential libatlas-base-dev libblas-dev openssl \ + bzip2 \ + ca-certificates \ + openjdk-8-jre-headless \ + tzdata \ + sudo \ wget zlib1g-dev nodejs && \ apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* -RUN npm install -g grunt-contrib-qunit grunt grunt-cli +RUN npm install -g grunt grunt-cli RUN mkdir -p /tmp/ansible && \ mkdir -p /opt/galaxy/db && \ @@ -70,7 +77,7 @@ RUN . $GALAXY_VIRTUAL_ENV/bin/activate && \ pip install mysql && \ cd $GALAXY_ROOT && \ echo "Prepopulating postgres database" && \ - su -c '/usr/lib/postgresql/9.3/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres && \ + su -c '/usr/lib/postgresql/${POSTGRES_MAJOR}/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres && \ sleep 3 && \ GALAXY_CONFIG_DATABASE_CONNECTION="postgresql://root@localhost:5930/galaxy" bash create_db.sh && \ echo "Prepopulating sqlite database" && \ diff --git a/test/docker/base/ansible_vars.yml b/test/docker/base/ansible_vars.yml index 96922310408..61387a5602f 100644 --- a/test/docker/base/ansible_vars.yml +++ b/test/docker/base/ansible_vars.yml @@ -4,8 +4,10 @@ galaxyFS_base_dir: /opt/galaxy # TODO: use GALAXY_ROOT via cmd line instead galaxy_server_dir: "/galaxy" galaxy_venv_dir: "{{ galaxyFS_base_dir }}/.venv" -galaxy_repo: https://bitbucket.org/galaxy/galaxy-central -galaxy_changeset_id: stable +galaxy_vcs: git +galaxy_git_repo: https://github.com/galaxyproject/galaxy.git +galaxy_changeset_id: dev +galaxy_download_url: https://codeload.github.com/galaxyproject/galaxy/tar.gz/dev galaxy_manage_clone: no galaxy_manage_download: yes galaxy_root: "{{ galaxy_server_dir}}" @@ -15,7 +17,7 @@ galaxy_db_log: /tmp/pSQL.log psql_galaxyftp_password: ignoredthis galaxy_config_file: "{{ galaxy_server_dir }}/config/galaxy.ini" configure_docker: no -postgresql_bin_dir: /usr/lib/postgresql/9.3/bin +postgresql_bin_dir: /usr/lib/postgresql/9.5/bin galaxy_manage_database: no galaxy_user_name: "root" diff --git a/test/docker/base/run_test_wrapper.sh b/test/docker/base/run_test_wrapper.sh index 7f1b9b70336..0149b4f4932 100644 --- a/test/docker/base/run_test_wrapper.sh +++ b/test/docker/base/run_test_wrapper.sh @@ -17,7 +17,7 @@ chown -R "$GALAXY_TEST_UID:$GALAXY_TEST_UID" /galaxy_venv : ${GALAXY_TEST_DATABASE_TYPE:-"postgres"} if [ "$GALAXY_TEST_DATABASE_TYPE" = "postgres" ]; then - su -c '/usr/lib/postgresql/9.3/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres + su -c '/usr/lib/postgresql/9.5/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres sleep 3 GALAXY_TEST_INSTALL_DB_MERGED="true" GALAXY_TEST_DBURI="postgres://root@localhost:5930/galaxy?client_encoding=utf8"