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GalaxyP Docker Image

The GalaxyP Community is devoted to the creation of excellent resources for proteomics research conducted through the Galaxy Project.

https://github.com/galaxyproteomics/tools-galaxyp

Usage

At first you need to install docker. Please follow the very good instructions from the Docker project.

After the successful installation, all what you need to do is:

  docker run -d -p 8080:80 -p 8021:21 quay.io/bgruening/galaxy-proteomics

I will shortly explain the meaning of all the parameters. For a more detailed description please consult the docker manual, it's really worth reading.
Let's start: docker run will run the Image/Container for you. In case you do not have the Container stored locally, docker will download it for you. -p 8080:80 will make the port 80 (inside of the container) available on port 8080 on your host. Same holds for port 8021, that can be used to transfer data via the FTP protocol. Inside the container a Apache Webserver is running on port 80 and that port can be bound to a local port on your host computer. With this parameter you can access your Galaxy instance via http://localhost:8080 immediately after executing the command above. bgruening/galaxyp is the Image/Container name, that directs docker to the correct path in the docker index. -d will start the docker container in daemon mode. For an interactive session, you can execute:

  docker run -i -t -p 8080:80  quay.io/bgruening/galaxy-proteomics /bin/bash

and run the startup script by yourself, to start PostgreSQL, Apache and Galaxy.

Docker images are "read-only", all your changes inside one session will be lost after restart. This mode is usefull to present Galaxy to your collegues or to run workshops with it. To install Tool Shed respositories or to save your data you need to export the calculated data to the host computer.

Fortunately, this is as easy as:

  docker run -d -p 8080:80 -v /home/user/galaxy_storage/:/export/ quay.io/bgruening/galaxy-proteomics

With the additional -v /home/user/galaxy_storage/:/export/ parameter, docker will mount the folder /home/user/galaxy_storage into the Container under /export/. A startup.sh script, that is usually starting Apache, PostgreSQL and Galaxy, will recognize the export directory with one of the following outcomes:

  • In case of an empty /export/ directory, it will move the PostgreSQL database, the Galaxy database directory, Shed Tools and Tool Dependencies and various config scripts to /export/ and symlink back to the original location.
  • In case of a non-empty /export/, for example if you continue a previous session within the same folder, nothing will be moved, but the symlinks will be created.

This enables you to have different export folders for different sessions - means real separation of your different projects.

Enabling Interactive Environments in Galaxy

Interactive Environments (IE) are sophisticated ways to extend Galaxy with powerful services, like IPython, in a secure and reproducible way.
For this we need to be able to launch Docker containers inside our Galaxy Docker container. At least docker 1.3 is needed on the host system.

  docker run -d -p 8080:80 -p 8021:21 -p 8800:8800 --privileged=true \
    -v /home/user/galaxy_storage/:/export/ quay.io/bgruening/galaxy-proteomics

The port 8800 is the proxy port that is used to handle Interactive Environments. --privileged is needed to start docker containers inside docker.

Using Parent docker

On some linux distributions, Docker-In-Docker can run into issues (such as running out of loopback interfaces). If this is an issue, you can use a 'legacy' mode that use a docker socket for the parent docker installation mounted inside the container. To engage, set the environmental variable DOCKER_PARENT

  docker run -p 8080:80 -p 8021:21 -p 8800:8800 \
    --privileged=true -e DOCKER_PARENT=True \
    -v /var/run/docker.sock:/var/run/docker.sock \
    -v /home/user/galaxy_storage/:/export/ \
    quay.io/bgruening/galaxy-proteomics

Galaxy Report Webapp

For admins wishing to have more information on the status of a galaxy instance, the Galaxy Report Webapp is served on http://localhost:8080/reports. As default this site is password protected with admin:admin. You can change this by providing a reports_htpasswd file in /home/user/galaxy_storage/.

You can disable the Report Webapp entirely by providing the environment variable NONUSE during container startup.

  docker run -p 8080:80 -e "NONUSE=reports" quay.io/bgruening/galaxy-proteomics

Galaxy's config settings

Every Galaxy configuration setting can be overwritten by a given environment variable during startup. For example by default the admin_users, master_api_key and the brand variable it set to:

  GALAXY_CONFIG_ADMIN_USERS=admin@galaxy.org
  GALAXY_CONFIG_MASTER_API_KEY=HSNiugRFvgT574F43jZ7N9F3
  GALAXY_CONFIG_BRAND="Galaxy Docker Build"

You can and should overwrite these during launching your container:

  docker run -p 8080:80 \
    -e "GALAXY_CONFIG_ADMIN_USERS=albert@einstein.gov" \
    -e "GALAXY_CONFIG_MASTER_API_KEY=83D4jaba7330aDKHkakjGa937" \
    -e "GALAXY_CONFIG_BRAND='My own Galaxy flavour'" \
    quay.io/bgruening/galaxy-proteomics

Personalize your Galaxy

The Galaxy welcome screen can be changed by providing a welcome.hml page in /home/user/galaxy_storage/. All files starting with welcome will be copied during starup and served as indroduction page. If you want to include images or other media, name them welcome_* and link them relative to your welcome.html (example).

Deactivating services

Non-essential services can be deactivated during startup. Set the environment variable NONUSE to a comma separated list of services. Currently, nodejs, proftp and reports are supported.

  docker run -d -p 8080:80 -p 8021:21 -p 9002:9002 \
    -e "NONUSE=nodejs,proftp,reports" quay.io/bgruening/galaxy-proteomics

A graphical user interface, to start and stop your services, is available on port 9002 if you run your container like above.

Restarting Galaxy

If you want to restart Galaxy without restarting the entire Galaxy container you can use docker exec (docker > 1.3).

  docker exec <container name> supervisorctl restart galaxy:

In addition you start/stop every supersisord process using a webinterface on port 9002. Start your container with:

  docker run -p 9002:9002 quay.io/bgruening/galaxy-proteomics

Advanced Logging

You can set the environment variable $GALAXY_LOGGING to FULL to access all logs from supervisor. For example start your container with:

  docker run -d -p 8080:80 -p 8021:21 -e "GALAXY_LOGGING=full" quay.io/bgruening/galaxy-proteomics

In addition you can access the supersisord webinterface on port 9002 and get access to log files. Start your container with:

  docker run -d -p 8080:80 -p 8021:21 -p 9002:9002 -e "GALAXY_LOGGING=full" quay.io/bgruening/galaxy-proteomics

Users & Passwords

The Galaxy Admin User has the username admin@galaxy.org and the password admin.
The PostgreSQL username is galaxy, the password is galaxy and the database name is galaxy (I know I was really creative ;)).
If you want to create new users, please make sure to use the /export/ volume. Otherwise your user will be removed after your docker session is finished.

The proftpd server is configured to use the main galaxy PostgreSQL user to access the database and select the username and password. If you want to run the
docker container in production, please do not forget to change the user credentials in /etc/proftp/proftpd.conf too.

The Galaxy Report Webapp is htpasswd protected with username and password st to admin.

Requirements

Support & Bug Reports

You can file an github issue or ask
us on the Galaxy development list.

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bgruening
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