diff --git a/.gitmodules b/.gitmodules index 3a7c2d3c4..29623c5ae 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,9 +1,6 @@ [submodule "galaxy/roles/galaxyproject.galaxyextras"] path = galaxy/roles/galaxyprojectdotorg.galaxyextras url = https://github.com/galaxyproject/ansible-galaxy-extras -[submodule "galaxy/roles/galaxy-tools-playbook"] - path = galaxy/roles/galaxy-tools-playbook - url = https://github.com/afgane/galaxy-tools-playbook [submodule "galaxy/roles/galaxy-postgresql"] path = galaxy/roles/galaxy-postgresql url = https://github.com/galaxyproject/ansible-postgresql diff --git a/.travis.yml b/.travis.yml index f4a34d85b..20c8299b8 100644 --- a/.travis.yml +++ b/.travis.yml @@ -76,7 +76,7 @@ script: # Test the 'old' tool installation script - docker run quay.io/bgruening/galaxy bash -c 'install-repository "--url https://toolshed.g2.bx.psu.edu -o iuc --name bedtools --panel-section-name 'BEDTools'"' # Test the 'new' tool installation script - - docker run quay.io/bgruening/galaxy bash -c "install-tools $GALAXY_HOME/ansible/galaxy-tools-playbook/files/sample_tool_list.yaml" + - docker run quay.io/bgruening/galaxy bash -c "install-tools $GALAXY_HOME/ephemeris/sample_tool_list.yaml" # Test Docker in Docker, used by Interactive Environments; This needs to be at the end as Docker takes some time to start. - docker exec -i -t galaxy docker info - docker stop galaxy diff --git a/galaxy/Dockerfile b/galaxy/Dockerfile index 3e8d4be5d..da7c54c38 100644 --- a/galaxy/Dockerfile +++ b/galaxy/Dockerfile @@ -11,7 +11,7 @@ MAINTAINER Björn A. Grüning, bjoern.gruening@gmail.com # * Enable the @natefoo magic # Web server infrastructure matching usegalaxy.org - supervisor, uwsgi, and nginx. -ENV GALAXY_RELEASE=dev \ +ENV GALAXY_RELEASE=release_16.07 \ GALAXY_REPO=https://github.com/galaxyproject/galaxy \ GALAXY_ROOT=/galaxy-central \ GALAXY_CONFIG_DIR=/etc/galaxy @@ -64,7 +64,7 @@ RUN apt-get -qq update && apt-get install --no-install-recommends -y apt-transpo apt-get install --no-install-recommends -y mercurial python-psycopg2 postgresql-9.3 sudo samtools python-virtualenv \ nginx-extras=1.4.6-1ubuntu3.4ppa1 nginx-common=1.4.6-1ubuntu3.4ppa1 uwsgi uwsgi-plugin-python supervisor lxc-docker-1.9.1 slurm-llnl slurm-llnl-torque libswitch-perl \ slurm-drmaa-dev proftpd proftpd-mod-pgsql libyaml-dev nodejs-legacy npm ansible \ - nano nmap lynx vim curl python-pip python-gnuplot python-rpy2 python-psutil condor python-ldap \ + nano nmap lynx vim curl python-crypto python-pip python-gnuplot python-rpy2 python-psutil condor python-ldap \ gridengine-common gridengine-drmaa1.0 && \ pip install --upgrade pip && \ pip install ephemeris && \ @@ -91,6 +91,7 @@ RUN mkdir $GALAXY_ROOT && \ RUN su $GALAXY_USER -c "cp $GALAXY_ROOT/config/galaxy.ini.sample $GALAXY_CONFIG_FILE" ADD ./reports_wsgi.ini.sample $GALAXY_CONFIG_DIR/reports_wsgi.ini +ADD sample_tool_list.yaml $GALAXY_HOME/ephemeris/sample_tool_list.yaml ADD roles/ /tmp/ansible/roles ADD provision.yml /tmp/ansible/provision.yml ADD postgresql_provision.yml /tmp/ansible/postgresql_provision.yml @@ -161,10 +162,10 @@ RUN ./scripts/common_startup.sh && \ # Install all required Node dependencies. This is required to get proxy support to work for Interactive Environments cd $GALAXY_ROOT/lib/galaxy/web/proxy/js && \ npm install && \ - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && \ - bash Miniconda3-latest-Linux-x86_64.sh -b -p $GALAXY_CONDA_PREFIX && \ - rm Miniconda3-latest-Linux-x86_64.sh && \ - $GALAXY_CONDA_PREFIX/bin/conda install conda==3.19.3 + wget https://repo.continuum.io/miniconda/Miniconda3-4.0.5-Linux-x86_64.sh && \ + bash Miniconda3-4.0.5-Linux-x86_64.sh -b -p $GALAXY_CONDA_PREFIX && \ + rm Miniconda3-4.0.5-Linux-x86_64.sh && \ + $GALAXY_CONDA_PREFIX/bin/conda install -y conda==3.19.3 # Container Style ADD GalaxyDocker.png $GALAXY_CONFIG_DIR/web/welcome_image.png @@ -189,10 +190,6 @@ RUN rm $PG_DATA_DIR_DEFAULT -rf && \ python /usr/local/bin/create_galaxy_user.py --user $GALAXY_DEFAULT_ADMIN_USER --password $GALAXY_DEFAULT_ADMIN_PASSWORD -c $GALAXY_CONFIG_FILE --key $GALAXY_DEFAULT_ADMIN_KEY && \ service postgresql stop -# Add Ansible playbook for installing tools -ADD roles/galaxy-tools-playbook $GALAXY_HOME/ansible/galaxy-tools-playbook -RUN chown -R $GALAXY_USER:$GALAXY_USER $GALAXY_HOME/ansible - # Activate additional Tool Sheds # Activate the Test Tool Shed during runtime, useful for testing repositories. ADD ./tool_sheds_conf.xml $GALAXY_HOME/tool_sheds_conf.xml diff --git a/galaxy/install_tools_wrapper.sh b/galaxy/install_tools_wrapper.sh index a9825adf8..4ee5992fc 100644 --- a/galaxy/install_tools_wrapper.sh +++ b/galaxy/install_tools_wrapper.sh @@ -47,13 +47,7 @@ else done fi -su galaxy -c "cd $GALAXY_HOME/ansible/galaxy-tools-playbook; unset PYTHONPATH; \ - ansible-playbook tools.yml -i "localhost," --extra-vars galaxy_tools_api_key=admin \ - --extra-vars galaxy_config_file=/etc/galaxy/galaxy.ini \ - --extra-vars galaxy_venv_dir=$GALAXY_VIRTUAL_ENV \ - --extra-vars galaxy_server_dir=/galaxy-central \ - --extra-vars galaxy_tools_galaxy_instance_url=localhost:$PORT \ - --extra-vars galaxy_tools_tool_list=$1" +shed-install -g "http://localhost:$PORT" -a admin -t "$1" exit_code=$? diff --git a/galaxy/roles/galaxy-tools-playbook b/galaxy/roles/galaxy-tools-playbook deleted file mode 160000 index a25348482..000000000 --- a/galaxy/roles/galaxy-tools-playbook +++ /dev/null @@ -1 +0,0 @@ -Subproject commit a253484822c0c1ea84c3136696702c1647e161e1 diff --git a/galaxy/sample_tool_list.yaml b/galaxy/sample_tool_list.yaml new file mode 100644 index 000000000..b20b61ec6 --- /dev/null +++ b/galaxy/sample_tool_list.yaml @@ -0,0 +1,11 @@ +# This is just a sample file. For a fully documented version of this file, see +# https://github.com/galaxyproject/ansible-galaxy-tools/blob/master/files/tool_list.yaml.sample +tools: +- name: 'column_maker' + owner: 'devteam' + tool_panel_section_label: 'Columnmaker section' +- name: 'tabular_to_fasta' + owner: 'devteam' + tool_panel_section_label: 'New Converters' + revisions: + - '0b4e36026794' # v1.1.0