Galaxy

An Ansible role for installing and managing Galaxy servers. Despite the name confusion, Galaxy bears no relation to Ansible Galaxy.

Requirements

This role has the same dependencies as the git module. In addition, Python virtualenv is required (as is pip, but pip will be automatically installed with virtualenv). These can easily be installed via a pre-task in the same play as this role:

- hosts: galaxyservers
  pre_tasks:
    - name: Install Dependencies
      apt:
        name: "{{ item }}"
      become: yes
      when: ansible_os_family == 'Debian'
      with_items:
        - git
        - python-virtualenv
    - name: Install Dependencies
      yum:
        name: "{{ item }}"
      become: yes
      when: ansible_os_family == 'RedHat'
      with_items:
        - mercurial
        - python-virtualenv
  roles:
    - galaxyproject.galaxy

If your git executable is not on $PATH, you can specify its location with the git_executable variable. Likewise with the virtualenv executable and corresponding galaxy_virtualenv_command variable.

Role Variables

Not all variables are listed or explained in detail. For additional information about less commonly used variables, see the defaults file.

Many variables control where specific files are placed and where Galaxy writes data. In order to simplify configuration, you may select a layout with the galaxy_layout variable. Which layout you choose affects the required variables.

Required variables

If using any layout other than root-dir:

• galaxy_server_dir: Filesystem path where the Galaxy server code will be installed (cloned).

If using root-dir:

• galaxy_root: Filesystem path of the root of a Galaxy deployment, the Galaxy server code will be installed in to a subdirectory of this directory.

Optional variables

Layout control

• galaxy_layout: available layouts can be found in the vars/ subdirectory and possible values include:
  • root-dir: Everything is laid out in subdirectories underneath a single root directory.
  • opt: An FHS-conforming layout across multiple directories such as /opt, /etc/opt, etc.
  • legacy-improved: Everything underneath the Galaxy server directory, as with run.sh.
  • legacy: The default layout prior to the existence of galaxy_layout and currently the default so as not to break existing usage of this role.
  • custom: Reasonable defaults for custom layouts, requires setting a few variables as described in vars/layout-custom.yml

Either the root-dir or opt layout is recommended for new Galaxy deployments.

Options below that control individual file or subdirectory placement can still override defaults set by the layout.

New options for Galaxy 18.01 and later

• galaxy_config_style (default: ini-paste): The type of Galaxy configuration file to write, ini-paste for the traditional PasteDeploy-style INI file, or yaml for the YAML format supported by uWSGI.
• galaxy_app_config_section (default: depends on galaxy_config_style): The config file section under which the Galaxy config should be placed (and the key in galaxy_config in which the Galaxy config can be found. If galaxy_config_style is ini-paste the default is app:main. If galaxy_config_style is yaml, the default is galaxy.
• galaxy_uwsgi_yaml_parser (default: internal): Controls whether the uwsgi section of the Galaxy config file will be written in uWSGI-style YAML or real YAML. By default, uWSGI's internal YAML parser does not support real YAML. Set to libyaml to write real YAML, if you are using uWSGI that has been compiled with libyaml. see YAML Syntax below and unbit/uwsgi#863 for details.

YAML Syntax

To override the default uWSGI configuration, place your uWSGI options under the uwsgi key in the galaxy_config dictionary explained below. Note that the defaults are not merged with your config, so you should fully define the uwsgi section if you choose to set it.

uWSGI's internal YAML parser expects YAML in an non-standards-conforming syntax:

• Quotes are not supported: all values are read as strings
• Multiple overlapping keys are used to specify multiple instances of an option
• Despite appearing to be a YAML dictionary, the order of the dictionary keys in the config is preserved

Note that regardless of which galaxy_uwsgi_yaml_parser you use, galaxy_config.uwsgi should be written in real YAML because Ansible parses it with libyaml, which does not support the uWSGI internal parser's invalid syntax. This role will automatically convert the proper YAML to uWSGI-style YAML as necessary.

In order to specify repeititve uWSGI options, the value of the option should be a list. For example, multiple mules for Galaxy handlers are specified like so:

galaxy_config:
  uwsgi:
    # a few example options
    socket: 127.0.0.1:4001
    master: true
    # define mules
    mule:
      - lib/galaxy/main.py
      - lib/galaxy/main.py
    farm: job-handlers:1,2

This role will convert the above to the proper uWSGI-style representation in galaxy.yml:

uwsgi:
    farm: job-handlers:1,2
    master: true
    mule: lib/galaxy/main.py
    mule: lib/galaxy/main.py
    socket: 127.0.0.1:4001

The value of galaxy_config.uwsgi can be either a hash (dictionary) of option/value pairs, or a list of one-item option/value hashes. In the former case, the options will be written to galaxy.yml in sorted order, since hashes do not maintain order. In the latter case, order is preserved, and allows for use of uWSGI's configuration logic, for which the order matters.

When specifying control logic such as if-* and for, the value of the option is a list where:

• The first list member is the conditional
• The remaining list members are the option/values in the control block
• Do not specify the closing endif or endfor, the role will do this for you

For example, to use if-exists as is commonly done for uWSGI Zerg Mode, use:

galaxy_config:
  uwsgi:
    # a few example options
    - socket: 127.0.0.1:4001
    - master: true
    # define master FIFOs
    - master-fifo:
      - /srv/galaxy/var/zerg-new.fifo
      - /srv/galaxy/var/zerg-run.fifo
      - /srv/galaxy/var/zerg-old.fifo
    # control block
    - if-exists:
      - /srv/galaxy/var/zerg-run.fifo
      - hook-accepting1-once: writefifo:/srv/galaxy/var/zerg-run.fifo 2q
    - hook-accepting1-once: writefifo:/srv/galaxy/var/zerg-new.fifo 1

The role converts this to the following galaxy.yml contents:

uwsgi:
    socket: 127.0.0.1:4001
    master: true
    master-fifo: /srv/galaxy/var/zerg-new.fifo
    master-fifo: /srv/galaxy/var/zerg-run.fifo
    master-fifo: /srv/galaxy/var/zerg-old.fifo
    if-exists: /srv/galaxy/var/zerg-run.fifo
    hook-accepting1-once: writefifo:/srv/galaxy/var/zerg-run.fifo 2q
    endif: null
    hook-accepting1-once: spinningfifo:/srv/galaxy/var/zerg-new.fifo 1

Feature control

Several variables control which functions this role will perform (all default to yes except where noted):

• galaxy_create_user (default: no): Create the Galaxy user. Running as a dedicated user is a best practice, but most production Galaxy instances submitting jobs to a cluster will manage users in a directory service (e.g. LDAP). This option is useful for standalone servers. Requires superuser privileges.
• galaxy_manage_paths (default: no): Create and manage ownership/permissions of configured Galaxy paths. Requires superuser privileges.
• galaxy_manage_clone: Clone Galaxy from the source repository and maintain it at a specified version (commit), as well as set up a [virtualenv][virtualenv] from which it can be run.
• galaxy_manage_static_setup: Manage "static" Galaxy configuration files - ones which are not modifiable by the Galaxy server itself. At a minimum, this is the primary Galaxy configuration file, galaxy.ini.
• galaxy_manage_mutable_setup: Manage "mutable" Galaxy configuration files - ones which are modifiable by Galaxy (e.g. as you install tools from the Galaxy Tool Shed).
• galaxy_manage_database: Upgrade the database schema as necessary, when new schema versions become available.
• galaxy_fetch_dependencies: Fetch Galaxy dependent modules to the Galaxy virtualenv.
• galaxy_build_client: Build the Galaxy client application (web UI).
• galaxy_client_make_target (default: client-production-maps): Set the client build type. Options include: client, client-production and client-production-maps. See Galaxy client readme for details.
• galaxy_manage_errordocs (default: no): Install Galaxy-styled 413 and 502 HTTP error documents for nginx. Requires write privileges for the nginx error document directory.

Galaxy code and configuration

Options for configuring Galaxy and controlling which version is installed.

• galaxy_config: The contents of the Galaxy configuration file (galaxy.ini by default) are controlled by this variable. It is a hash of hashes (or dictionaries) that will be translated in to the configuration file. See the Example Playbooks below for usage.
• galaxy_config_files: List of hashes (with src and dest keys) of files to copy from the control machine.
• galaxy_config_templates: List of hashes (with src and dest keys) of templates to fill from the control machine.
• galaxy_local_tools: List of local tool files or directories to copy from the control machine, relative to galaxy_local_tools_src_dir (default: files/galaxy/tools in the playbook).
• galaxy_local_tools_dir: Directory on the Galaxy server where local tools will be installed.
• galaxy_dynamic_job_rules: List of dynamic job rules to copy from the control machine, relative to galaxy_dynamic_job_rules_src_dir (default: files/galaxy/dynamic_job_rules in the playbook).
• galaxy_dynamic_job_rules_dir (default: {{ galaxy_server_dir }}/lib/galaxy/jobs/rules): Directory on the Galaxy server where dynamic job rules will be installed. If changed from the default, ensure the directory is on Galaxy's $PYTHONPATH (e.g. in {{ galaxy_venv_dir }}/lib/python2.7/site-packages) and configure the dynamic rules plugin in job_conf.xml accordingly.
• galaxy_repo (default: https://github.com/galaxyproject/galaxy.git): Upstream Git repository from which Galaxy should be cloned.
• galaxy_commit_id (default: master): A commit id, tag, branch, or other valid Git reference that Galaxy should be updated to. Specifying a branch will update to the latest commit on that branch. Using a real commit id is the only way to explicitly lock Galaxy at a specific version.
• galaxy_force_checkout (default: no): If yes, any modified files in the Galaxy repository will be discarded.
• galaxy_clone_depth (default: null): Depth to use when performing git clone. Leave unspecified to clone entire history.

Path configuration

Options for controlling where certain Galaxy components are placed on the filesystem.

• galaxy_venv_dir (default: <galaxy_server_dir>/.venv): The role will create a [virtualenv][virtualenv] from which Galaxy will run, this controls where the virtualenv will be placed.
• galaxy_config_dir (default: <galaxy_server_dir>): Directory that will be used for "static" configuration files.
• galaxy_mutable_config_dir (default: <galaxy_server_dir>): Directory that will be used for "mutable" configuration files, must be writable by the user running Galaxy.
• galaxy_mutable_data_dir (default: <galaxy_server_dir>/database): Directory that will be used for "mutable" data and caches, must be writable by the user running Galaxy.
• galaxy_config_file (default: <galaxy_config_dir>/galaxy.ini): Galaxy's primary configuration file.

User management and privilege separation

• galaxy_separate_privileges (default: no): Enable privilege separation mode.
• galaxy_user (default: user running ansible): The name of the system user under which Galaxy runs.
• galaxy_privsep_user (default: root): The name of the system user that owns the Galaxy code, config files, and virtualenv (and dependencies therein).
• galaxy_group: Common group between the Galaxy user and privilege separation user. If set and galaxy_manage_paths is enabled, directories containing potentially sensitive information such as the Galaxy config file will be created group- but not world-readable. Otherwise, directories are created world-readable.

Access method control

The role needs to perform tasks as different users depending on which features you have enabled and how you are connecting to the target host. By default, the role will use become (i.e. sudo) to perform tasks as the appropriate user if deemed necessary. Overriding this behavior is discussed in the defaults file.

Error documents

• galaxy_errordocs_dir: Install Galaxy-styled HTTP 413 and 502 error documents under this directory. The 502 message uses nginx server side includes to allow administrators to create a custom message in ~/maint when Galaxy is down. nginx must be configured separately to serve these error documents.
• galaxy_errordocs_server_name (default: Galaxy): used to display the message "galaxy_errdocs_server_name cannot be reached" on the 502 page.
• galaxy_errordocs_prefix (default: /error): Web-side path to the error document root.

Miscellaneous options

• galaxy_restart_handler_name: The role doesn't restart Galaxy since it doesn't control how Galaxy is started and stopped. Because of this, you can write your own restart handler and inform the role of your handler's name with this variable. See the examples
• galaxy_admin_email_to: If set, email this address when Galaxy has been updated. Assumes mail is properly configured on the managed host.
• galaxy_admin_email_from: Address to send the aforementioned email from.

Dependencies

None

Example Playbook

Basic

Install Galaxy on your local system with all the default options:

- hosts: localhost
  vars:
    galaxy_server_dir: /srv/galaxy
  connection: local
  roles:
     - galaxy

Once installed, you can start with:

$ cd /srv/galaxy
$ sh run.sh

Best Practice

Install Galaxy as per the current production server best practices:

• Galaxy code (clone) is "clean": no configs or mutable data live underneath the clone
• Galaxy code and static configs are privilege separated: not owned/writeable by the user that runs Galaxy
• Configuration files are not world-readable
• PostgreSQL is used as the backing database
• The 18.01+ style YAML configuration is used
• Two job handler mules are started
• When the Galaxy code or configs are updated by Ansible, Galaxy will be restarted using supervisorctl

- hosts: galaxyservers
  vars:
    galaxy_config_style: yaml
    galaxy_layout: root-dir
    galaxy_root: /srv/galaxy
    galaxy_commit_id: release_18.09
    galaxy_separate_privileges: yes
    galaxy_create_user: yes
    galaxy_manage_paths: yes
    galaxy_user: galaxy
    galaxy_privsep_user: gxpriv
    galaxy_group: galaxy
    galaxy_restart_handler_name: Restart Galaxy
    postgresql_objects_users:
      - name: galaxy
        password: null
    postgresql_objects_databases:
      - name: galaxy
        owner: galaxy
    galaxy_config:
      uwsgi:
        socket: 127.0.0.1:4001
        buffer-size: 16384
        processes: 1
        threads: 4
        offload-threads: 2
        static-map:
          - /static/style={{ galaxy_server_dir }}/static/style/blue
          - /static={{ galaxy_server_dir }}/static
        master: true
        virtualenv: "{{ galaxy_venv_dir }}"
        pythonpath: "{{ galaxy_server_dir }}/lib"
        module: galaxy.webapps.galaxy.buildapp:uwsgi_app()
        thunder-lock: true
        die-on-term: true
        hook-master-start:
          - unix_signal:2 gracefully_kill_them_all
          - unix_signal:15 gracefully_kill_them_all
        py-call-osafterfork: true
        enable-threads: true
        mule:
          - lib/galaxy/main.py
          - lib/galaxy/main.py
        farm: job-handlers:1,2
      galaxy:
        database_connection: "postgresql:///galaxy?host=/var/run/postgresql"
  pre_tasks:
    - name: Install Dependencies
      apt:
        name: ['git', 'python-psycopg2', 'python-virtualenv']
      become: yes
  roles:
    # Install with:
    #   % ansible-galaxy install galaxyproject.postgresql
    - role: galaxyproject.postgresql
      become: yes
    # Install with:
    #   % ansible-galaxy install natefoo.postgresql_objects
    - role: natefoo.postgresql_objects
      become: yes
      become_user: postgres
    - role: galaxyproject.galaxy
  handlers:
    - name: Restart Galaxy
      supervisorctl:
        name: galaxy
        state: restarted

License

Academic Free License ("AFL") v. 3.0

Author Information

This role was written and contributed to by the following people:

• Enis Afgan
• Dannon Baker
• Simon Belluzzo
• John Chilton
• Nate Coraor
• Helena Rasche