Configuring galaxy instance for a vm

On this page you can find all information on configuring the galaxy instance.

Setting up the galaxy host

  1. Set up a (virtual) server running one of the supported distributions. galaxy-launcher is tested on the following distributions:
  2. Ubuntu 16.04 LTS
  3. CentOS 7.2
  4. Set up a passwordless sudo user on the remote host and set up an ssh key pair.
  5. NOTE: a passwordless sudo user is required on the remote host to perform rsync synchronization between the ansible-control host and the remote host.
  6. Make a new hosts file by copying hosts.sample to hosts and setup your galaxy host.
  7. Create a new configuration directory by copying host_vars/example_host to host_vars/HOSTNAME. Hostname should be equal to that specified in hosts
  8. Create a new files directory by copying files/example_host to files/HOSTNAME

Configuration locations

In hosts the ip address, hostname and remote user of the host can be defined. Settings files are located in host_vars/HOSTNAME. These files are all read by ansible for use as variables. In files/HOSTNAME all the files that are transferred to the host are stored.

Configuring your installation.

Settings files are located in host_vars/HOSTNAME. docker_settings.yml, galaxy_settings.yml and port_settings.yml should be checked and if necessary changed. Also tool lists can be added to install a set of tools.

docker_settings.yml

Variable Function
installdocker_default_location Where docker stores the images and containers. Use a volume with ample disk space.
galaxy_docker_docker_image The docker image. Defaults to "bgruening/galaxy-stable:latest" but it's better to tag it with a version number. (i.e. 17.09)
docker_user a user that will be created without sudo rights on the remote machine.
galaxy_docker_container_name What name the container gets for easy access using docker commands. Default is "galaxy".

galaxy_settings.yml

Variable Function
galaxy_admin_user e-mail address of the admin user. This variable is obligatory
galaxy_master_api_key The master api key. Always set this value to something unique.
galaxy_brand The galaxy brand name
galaxy_report_user The user to access the reports section.
galaxy_report_password The password to access the reports section.
galaxy_docker_optional_environment_settings This is a YAML dictionary that takes any docker environment values. See the documentation of bgruening/docker-galaxy-stable which options are available.

web_settings.yml

Variable Function
galaxy_docker_web_urls Nginx reroutes traffic coming from these urls to the galaxy server. You should put the registered domain name here.
max_upload_size The maximum sizes of files that can be uploaded.
galaxy_docker_web_port_public default 80. The web port for the nginx server.
galaxy_docker_web_port default 8080. This port is only exposed to localhost and not accessible from the web.
galaxy_docker_ftp_port By default this variable is not set and port is unaccessible. This port is only exposed to localhost and not accessible from the web.
galaxy_docker_sftp_port By default this variable is not set and port is unaccessible. This port is only exposed to localhost and not accessible from the web.

It is not recommended to touch the nginx settings unless you are familiar with configuring ansible-role-nginx.

backup_settings.yml

galaxy_docker_backup_location: "backup/location/path"

galaxy_docker_backup_rsync_remote_host: True # Enables or disables rsyncing all the backups to a remote host.


galaxy_docker_backup_database_cron_jobs:  
  daily: # The key is the "name" of the cron job  
    description: "Description of the cron job"  
    timestamp: "-%Z%Y%m%dT%H%M%S" # Timestamp uses the "date" function. Check date --help on how to use the timestamp  
    filename: "galaxy-hourly-backup" # Archives are stored as filename.timestamp.gz  
    files_to_keep: 7 # How many backups of this job should be kept. Since this jobs runs daily, one week of backups is kept  
    compression_level: 6 # Compression uses gzip. 6 is the default level.Level should be 1-9  
    cron: # This is a dictionary that uses the same values as the ansible cron module(http://docs.ansible.com/ansible/cron_module.html)   
      special_time: "daily"  
  two_weekly_example:  
    description: "Two-weekly backup of the galaxy database"  
    timestamp: "-%Z%Y%m%dT%H%M"  
    filename: "galaxy-fortnight-backup"  
    files_to_keep: 6  
    compression_level: 6  
    cron:
      month: *
      day: 1,15
      hour: 3

galaxy_docker_backup_database_rsync_settings:  
  dest: "/destination/path/on/remote/host"   
  host: "example.host.org"
  user: "user" # The user that is connected to. This key can be ommited
  delete: True # Remove backups on the remote server if they are removed on the galaxy server. True is recommended.
  compression_level: 0 # Can range from 0-9. Rsync compresses the data before transmission to save bandwith*
  cron:  How often the rsync to the remote host should be performed. Hourly is recommended.
    special_time: hourly #

 #* 0 is recommended because the archives are already compressed

Personalization (optional)

See bgruening/docker-galaxy-stable documentation.

Welcome files can be placed in files\HOSTNAME\welcome. This path can be changed in files_settings.yml.

Extra tools (optional)

Tool lists can be added to files/HOSTNAME/tools. To change this directory change galaxy_docker_tool_list_dir in files_settings.yml An example tool list can be found in files/example_host/tools. If no tool lists are present, this step will be automatically skipped. Only .yml and .yaml files are copied to the server.

Adding reference genomes (optional)

  1. Add reference genomes to be copied to the server (see below)
  2. Specify which data managers to run (see below)
  3. Make sure data managers specified are installed (see Extra tools section)
  4. Create an admin api key by logging in as the admin user and creating an API key. Because an admin api key is needed, this task cannot be completed during the run=install step.
  5. Run the installgenomes task. Reference genomes can be added to files/HOSTNAME/genomes. To change this directory change genome_dir in files_settings.yml.
    The genomes are copied to the server using rsync. Ownership information will not be kept and genomes will be world-readable.

In order to install the genomes a YAML file specifying the data managers that should be run should be placed in files/HOSTNAME/dbkeys. An example is included as run-data-managers.yaml.sample. Only .yml and .yaml files are copied to the server.

Configuring LDAP (optional)

Add a GALAXY_CONFIG_AUTH_CONFIG_FILE key to galaxy_docker_optional_environment_settings in host_vars/HOSTNAME/galaxy_settings.yml :

galaxy_docker_optional_environment_settings:
  GALAXY_CONFIG_AUTH_CONFIG_FILE: "config/auth_conf.xml"

In host_vars/HOSTNAME/ldap_settings.yml set the following keys in galaxy_docker_ldap_settings:

Keys required

Key Function
server The ldap server. (ldap://ad.example.com)
search_base example: dc=ad,dc=example,dc=com
search_user example: ldapsearch
search_password ldapsearch's password

Default keys (can optionally be changed)

Key Function Default
login_use_username Whether username is used. If False e-mail is used True
allow_password_change Whether users can change their password False
allow_register Whether users can register their own accounts. This bypasses ldap authentication. False
auto_register Users are automatically registered at first succesfull authentication to the LDAP server True
continue_on_failure login despite authentication module failures False
email_suffix The e-mail - suffix (@example.com). All users with such an address will be passed to the ldap server. If "" all users will be passed to the ldap server ""

Example

galaxy_docker_ldap_settings:
  server: "ldap://dc1.example.com"
  search_base: "dc=dc1,dc=example,dc=com"
  search_user: "ldapsearch"
  search_password: "supersecret" #ldapsearch's password
  login_use_username: False
  email_suffix: "@example.com"

Database (optional)

If you wish to use a postgresql database of another galaxy instance, make a dump of the instance. Put the dump file in files/HOSTNAME/database_import. Alternatively you can specify the location by changing galaxy_docker_import_db_dir in files_settings.yml If no database is added, a new empty DB will be created.