Merge pull request #7439 from mvdbeek/new_testing_image

New testing image

run_tests.sh

@@ -270,7 +270,7 @@ exists() {
     type "$1" >/dev/null 2>/dev/null
 }
 
-DOCKER_DEFAULT_IMAGE='galaxy/testing-base:19.01.0'
+DOCKER_DEFAULT_IMAGE='galaxy/testing-base:19.05.0'
 
 test_script="./scripts/functional_tests.py"
 report_file="run_functional_tests.html"

test/base/integration_util.py

@@ -33,10 +33,6 @@ def skip_unless_docker():
     return skip_unless_executable("docker")
 
 
-def skip_unless_singularity():
-    return skip_unless_executable("singularity")
-
-
 def skip_unless_kubernetes():
     return skip_unless_executable("kubectl")
 

test/docker/base/Dockerfile

@@ -19,34 +19,30 @@ ENV DEBIAN_FRONTEND=noninteractive \
 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://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add - && \
-    curl -s https://deb.nodesource.com/gpgkey/nodesource.gpg.key | apt-key add - && \
-    curl -sL https://deb.nodesource.com/setup_8.x | bash -  && \
     echo "deb http://dl.google.com/linux/chrome/deb/ stable main" >> /etc/apt/sources.list.d/google-chrome.list && \
+    curl -s http://neuro.debian.net/lists/xenial.us-ca.full > /etc/apt/sources.list.d/neurodebian.sources.list && \
+    apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9 && \
     apt-get update -y && \
-    apt-get install -y libpq-dev postgresql postgresql-client ansible wget \
-            slurm-llnl libmunge-dev slurm-drmaa-dev ant cmake curl \
-            g++ gcc gfortran git-core libffi-dev liblapack-dev \
-            libncurses5-dev libopenblas-dev libpam0g-dev libpq-dev libsparsehash-dev make \
-            patch postgresql postgresql \
-            postgresql-client python-dev python3-dev \
-            python-prettytable python-psycopg2 python-virtualenv python-pip \
-            rsync slurm-drmaa-dev swig sysstat unzip \
-            autoconf automake build-essential libatlas-base-dev libblas-dev openssl \
-            bzip2 uuid-dev libssl-dev libgpgme11-dev squashfs-tools libseccomp-dev pkg-config \
+    apt-get install -y --no-install-recommends postgresql postgresql-client ansible wget \
+            python3-dev \
+            git-core \
+            python-prettytable python-virtualenv python-pip \
+            rsync swig sysstat unzip \
+            openssl \
+            bzip2 \
             ca-certificates \
             openjdk-8-jre-headless \
             tzdata \
             sudo \
             locales \
             xvfb \
             ${CHROME_VERSION:-google-chrome-stable} \
-            wget zlib1g-dev nodejs \
+            ffmpeg \
+            bcftools \
+            singularity-container \
             libnss3 libgconf-2-4 && \
     apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
-# Install golang
-RUN export VERSION=1.11 OS=linux ARCH=amd64 && curl -sL https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz \
-    | tar -C /usr/local -xzf -
 
 RUN mkdir -p /tmp/ansible && \
     mkdir -p /opt/galaxy/db && \
@@ -76,7 +72,7 @@ RUN cd $GALAXY_ROOT && \
     virtualenv -p /usr/bin/python3 $GALAXY_VIRTUAL_ENV_3 && \
     for VENV in $GALAXY_VIRTUAL_ENV_2 $GALAXY_VIRTUAL_ENV_3; do \
         export GALAXY_VIRTUAL_ENV=$VENV && \
-        ./scripts/common_startup.sh || { echo "common_startup.sh failed"; exit 1; } && \
+        ./scripts/common_startup.sh && \
         dev_requirements=./lib/galaxy/dependencies/dev-requirements.txt && \
         [ -f $dev_requirements ] && $VENV/bin/pip install -r $dev_requirements; done
 
@@ -96,16 +92,6 @@ RUN for VENV in $GALAXY_VIRTUAL_ENV_3 $GALAXY_VIRTUAL_ENV_2; do \
     echo "Prepopulating toolshed sqlite database" && \
     TOOL_SHED_CONFIG_DATABASE_CONNECTION="sqlite:////opt/galaxy/toolshed.sqlite" bash create_db.sh tool_shed
 
-# 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 Selenium user with passwordless sudo
 #========================================
@@ -126,18 +112,6 @@ RUN  sudo mkdir -p /opt/selenium \
   && wget --no-verbose https://selenium-release.storage.googleapis.com/3.6/selenium-server-standalone-3.6.0.jar \
     -O /opt/selenium/selenium-server-standalone.jar
 
-USER seluser
-
-RUN export GOPATH=${HOME}/go && export PATH=/usr/local/go/bin:${PATH}:${GOPATH}/bin && \
-    mkdir -p $GOPATH/src/github.com/sylabs && \
-    cd $GOPATH/src/github.com/sylabs && \
-    git clone https://github.com/sylabs/singularity.git && \
-    cd singularity && \
-    git checkout v3.0.1 && \
-    ./mconfig && \
-    cd builddir && make && sudo make install && \
-    rm -Rf ${HOME}/go
-
 USER root
 
 #==============================

test/docker/base/ansible_vars.yml

@@ -3,7 +3,7 @@ add_system_users: no
 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_venv_dir: "/galaxy_venv"
 galaxy_vcs: git
 galaxy_git_repo: https://github.com/galaxyproject/galaxy.git
 galaxy_changeset_id: dev
@@ -24,6 +24,7 @@ install_maintainance_packages: false
 galaxy_user_name: "root"
 galaxy_extras_install_packages: true
 galaxy_job_conf_path: "/etc/galaxy/job_conf.xml"
+galaxy_build_client: no
 
 galaxy_web_processes: 1
 galaxy_handler_processes: 2

test/integration/test_containerized_jobs.py

@@ -31,7 +31,6 @@ def test_mulled_simple(self):
         assert "0.7.15-r1140" in output
 
 
-@integration_util.skip_unless_docker()
 class DockerizedJobsIntegrationTestCase(integration_util.IntegrationTestCase, RunsEnvironmentJobs, MulledJobTestCases):
 
     framework_tool_and_types = True