|galaxy_docker| instance ======================== The |project_name| Galaxy Docker application run a Galaxy Docker container inside a Centos 7 virtual machine. The `Official Galaxy Docker image `_ is used. Currently, |project_name| supports the following Docker images: - `bgruening/galaxy-stable `_ - `laniakeacloud/galaxy-covacs `_ - `laniakeacloud/galaxy-gdc_somatic_variant `_ - `bgruening/galaxy-rna-workbench `_ - `laniakeacloud/galaxy-epigen `_ .. note:: Docker is configured to install all docker-engine files on ``/export``, i.e. in the external storage. Configuration files ------------------- The Docker configuration is slighty customized to make the Galaxy experience as similar as possible to the one on the virtual machine. - ``/etc/galaxy/.myenv.sh``: file with the environment variables of the Docker container. The customized variables are: ``GALAXY_CONFIG_TOOL_DATA_TABLE_CONFIG_PATH``: tool_data_table_conf.xml specific for the galaxy flavour (see section :doc:`/user_documentation/galaxy/galaxy_flavours`) ``GALAXY_CONFIG_ADMIN_USERS``: admin_user - the email selected in the laniakea dashboard ``GALAXY_CONFIG_BRAND``: Galaxy brand - the **Instance description** inserted in the laniakea dashboard ``GALAXY_CONFIG_REQUIRE_LOGIN``: true - avoid anonymous login. ``GALAXY_CONFIG_ALLOW_USER_CREATION``: true - allow user creation. ``GALAXY_CONFIG_ALLOW_USER_IMPERSONATION``: false - allow user impersonation. ``GALAXY_CONFIG_NEW_USER_DATASET_ACCESS_ROLE_DEFAULT_PRIVATE``: true - By default, users' data will be public, but setting this to True will cause it to be private. ``GALAXY_CONDA_PREFIX``: path to _conda prefix ``GALAXY_CONFIG_CONDA_AUTO_INIT``: true - conda auto-start ``GALAXY_CONFIG_CONDA_AUTO_INSTALL``: true - conda auto-install - ``/etc/galaxy/tool_data_tables``: directory with the tool_data_table_conf.xml files. A detailed description of Laniakea Galaxy flavours configuration for the reference data is here: :doc:`/user_documentation/galaxy/galaxy_flavours`. CVMFS configuration ------------------- The CVMFS repository selected in the Lanikaea dashboard is automatically configured and mounted inside the docker directory ``/cvmfs``. The corresponding configuration files are in the directory ``/etc/cvmfs``. Galaxy docker usage ------------------- Galaxy docker logs ****************** SSH login in the virtual machine and type: :: $ sudo docker logs --tail 200 -f galaxydocker Enter in the Docker ******************* In order to access to the Galaxy container, SSH login in the virtual machine and execute the following command: :: $ sudo docker exec -it galaxydocker bash Main directories in the Docker ****************************** Main Galaxy directories inside the Docker container are in ``/export``: - ftp: ``/export/ftp`` - database: ``/export/database`` - conda: ``/export/tool_deps/_conda`` Check Galaxy configuration ************************** In order to see the Galaxy Docker configuration, SSH login in the virtual machine and execute the following command: :: $ sudo docker exec -it galaxydocker echo $GALAXY_CONFIG Data upload: FTP **************** Of course, the Galaxy Docker container allows user to upload data through FTP. The procedure is similar to that described in the ``Proftpd`` section here: :doc:`/user_documentation/galaxy_production_environment/galaxy_production_environment_configuration.rst`. Moreover, you need to enable FTP Passive mode. Go to ``Settings...``, then to ``FTP`` and flag ``Passive (recommended)``, as shown in the following picture. .. figure:: img/docker_ftp_passive.png :scale: 20 % :align: center For those using the command line tool, you can enable/disable the passive mode by typing ``passive``. First connect to the server then type: :: passive and you will be in passive mode. Galaxy Docker usage tutorial ---------------------------- .. raw:: html