Galaxy Docker instance¶
The Laniakea Galaxy Docker application run a Galaxy Docker container inside a Centos 7 virtual machine. The Official Galaxy Docker image is used. Currently, Laniakea 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 Galaxy Flavours)GALAXY_CONFIG_ADMIN_USERS
: admin_user - the email selected in the laniakea dashboardGALAXY_CONFIG_BRAND
: Galaxy brand - the Instance description inserted in the laniakea dashboardGALAXY_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 prefixGALAXY_CONFIG_CONDA_AUTO_INIT
: true - conda auto-startGALAXY_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: 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: /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.
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.