Name: docker-galaxy-stable
Owner: Biological Informatics CoE @ Agriculture and Agri-Food Canada
Owner: Biological Informatics CoE @ Agriculture and Agri-Food Canada
Description: :whale::bar_chart::books: Docker Images tracking the stable Galaxy releases.
Forked from: bgruening/docker-galaxy-stable
Created: 2015-07-21 15:42:27.0
Updated: 2016-11-07 18:39:41.0
Pushed: 2016-11-07 18:39:39.0
Size: 440
Language: Python
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The Galaxy Docker Image is an easy distributable full-fledged Galaxy installation, that can be used for testing, teaching and presenting new tools and features.
One of the main goals is to make the access to entire tool suites as easy as possible. Usually, this includes the setup of a public available webservice that needs to be maintained, or that the Tool-user needs to either setup a Galaxy Server by its own or to have Admin access to a local Galaxy server. With docker, tool developers can create their own Image with all dependencies and the user only needs to run it within docker.
The Image is based on Ubuntu 14.04 LTS and all recommended Galaxy requirements are installed. The following chart should illustrate the Docker image hierarchy we have build to make is as easy as possible to build on different layers of our stack and create many exciting Galaxy flavours.
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:
cker run -d -p 8080:80 -p 8021:21 bgruening/galaxy-stable
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/galaxy-stable 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:
cker run -i -t -p 8080:80 bgruening/galaxy-stable /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:
cker run -d -p 8080:80 -v /home/user/galaxy_storage/:/export/ bgruening/galaxy-stable
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:
/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./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.
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.
cker run -d -p 8080:80 -p 8021:21 -p 8800:8800 --privileged=true \
-v /home/user/galaxy_storage/:/export/ bgruening/galaxy-stable
The port 8800 is the proxy port that is used to handle Interactive Environments. --privileged is needed to start docker containers inside docker.
By default, FTP servers running inside of docker containers are not accessible via passive mode FTP, due to not being able to expose extra ports. To circumvent this, you can use the --net=host option to allow Docker to directly open ports on the host server:
cker run -d --net=host -v /home/user/galaxy_storage/:/export/ bgruening/galaxy-stable
Note that there is no need to specifically bind individual ports (e.g., -p 80:80).
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
cker 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/ \
bgruening/galaxy-stable
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.
cker run -p 8080:80 -e "NONUSE=reports" bgruening/galaxy-stable
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:
LAXY_CONFIG_ADMIN_USERS=admin@galaxy.org
LAXY_CONFIG_MASTER_API_KEY=HSNiugRFvgT574F43jZ7N9F3
LAXY_CONFIG_BRAND="Galaxy Docker Build"
You can and should overwrite these during launching your container:
cker 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'" \
bgruening/galaxy-stable
Note that if you would like to run any of the cleanup scripts, you will need to add the following to /export/galaxy-central/config/galaxy.ini:
database_connection = postgresql://galaxy:galaxy@localhost:5432/galaxy
file_path = /export/galaxy-central/database/files
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).
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.
cker run -d -p 8080:80 -p 8021:21 -p 9002:9002 \
-e "NONUSE=nodejs,proftp,reports" bgruening/galaxy-stable
A graphical user interface, to start and stop your services, is available on port 9002 if you run your container like above.
If you want to restart Galaxy without restarting the entire Galaxy container you can use docker exec (docker > 1.3).
cker exec <container name> supervisorctl restart galaxy:
In addition you start/stop every supersisord process using a webinterface on port 9002. Start your container with:
cker run -p 9002:9002 bgruening/galaxy-stable
You can set the environment variable $GALAXY_LOGGING to FULL to access all logs from supervisor. For example start your container with:
cker run -d -p 8080:80 -p 8021:21 -e "GALAXY_LOGGING=full" bgruening/galaxy-stable
In addition you can access the supersisord webinterface on port 9002 and get access to log files. Start your container with:
cker run -d -p 8080:80 -p 8021:21 -p 9002:9002 -e "GALAXY_LOGGING=full" bgruening/galaxy-stable
If your tools are already included in the Tool Shed, building your own personalised Galaxy docker Image (Galaxy flavour) can be done using the following steps:
DockerfileFROM bgruening/galaxy-stable at the top of the file. This means that you use the Galaxy Docker Image as base Image and build your own extensions on top of it.install_tool_shed_repositories.py script.docker build -t='my-docker-test'docker run -p 8080:80 my-docker-testhttp://localhost:8080For example have a look at the deepTools or the ChemicalToolBox Dockerfile's.
laxy - deepTools
RSION 0.2
bgruening/galaxy-stable
TAINER Björn A. Grüning, bjoern.gruening@gmail.com
GALAXY_CONFIG_BRAND deepTools
DIR /galaxy-central
stall deepTools
install-repository \
"--url https://toolshed.g2.bx.psu.edu/ -o bgruening --name deeptools"
rk folders as imported from the host.
ME ["/export/", "/data/", "/var/lib/docker"]
pose port 80 (webserver), 21 (FTP server), 8800 (Proxy)
SE :80
SE :21
SE :8800
tostart script that is invoked during container start
["/usr/bin/startup"]
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.
This repository uses a git submodule to include Ansible roles maintained by the Galaxy project.
You can clone this repository and the Ansible submodule with:
t clone --recursive https://github.com/bgruening/docker-galaxy-stable.git
Updating already existing submodules is possible with:
t submodule update --remote
You can file an github issue or ask us on the Galaxy development list.
The Galaxy Docker Image is an easy distributable full-fledged Galaxy installation, that can be used for testing, teaching and presenting new tools and features.
One of the main goals is to make the access to entire tool suites as easy as possible. Usually, this includes the setup of a public available webservice that needs to be maintained, or that the Tool-user needs to either setup a Galaxy Server by its own or to have Admin access to a local Galaxy server. With docker, tool developers can create their own Image with all dependencies and the user only needs to run it within docker.
The Image is based on Ubuntu 14.04 LTS and all recommended Galaxy requirements are installed. The following chart should illustrate the Docker image hierarchy we have build to make is as easy as possible to build on different layers of our stack and create many exciting Galaxy flavours.
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:
cker run -d -p 8080:80 -p 8021:21 bgruening/galaxy-stable
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/galaxy-stable 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:
cker run -i -t -p 8080:80 bgruening/galaxy-stable /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:
cker run -d -p 8080:80 -v /home/user/galaxy_storage/:/export/ bgruening/galaxy-stable
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:
/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./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.
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.
cker run -d -p 8080:80 -p 8021:21 -p 8800:8800 --privileged=true \
-v /home/user/galaxy_storage/:/export/ bgruening/galaxy-stable
The port 8800 is the proxy port that is used to handle Interactive Environments. --privileged is needed to start docker containers inside docker.
By default, FTP servers running inside of docker containers are not accessible via passive mode FTP, due to not being able to expose extra ports. To circumvent this, you can use the --net=host option to allow Docker to directly open ports on the host server:
cker run -d --net=host -v /home/user/galaxy_storage/:/export/ bgruening/galaxy-stable
Note that there is no need to specifically bind individual ports (e.g., -p 80:80).
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
cker 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/ \
bgruening/galaxy-stable
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.
cker run -p 8080:80 -e "NONUSE=reports" bgruening/galaxy-stable
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:
LAXY_CONFIG_ADMIN_USERS=admin@galaxy.org
LAXY_CONFIG_MASTER_API_KEY=HSNiugRFvgT574F43jZ7N9F3
LAXY_CONFIG_BRAND="Galaxy Docker Build"
You can and should overwrite these during launching your container:
cker 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'" \
bgruening/galaxy-stable
Note that if you would like to run any of the cleanup scripts, you will need to add the following to /export/galaxy-central/config/galaxy.ini:
database_connection = postgresql://galaxy:galaxy@localhost:5432/galaxy
file_path = /export/galaxy-central/database/files
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).
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.
cker run -d -p 8080:80 -p 8021:21 -p 9002:9002 \
-e "NONUSE=nodejs,proftp,reports" bgruening/galaxy-stable
A graphical user interface, to start and stop your services, is available on port 9002 if you run your container like above.
If you want to restart Galaxy without restarting the entire Galaxy container you can use docker exec (docker > 1.3).
cker exec <container name> supervisorctl restart galaxy:
In addition you start/stop every supersisord process using a webinterface on port 9002. Start your container with:
cker run -p 9002:9002 bgruening/galaxy-stable
You can set the environment variable $GALAXY_LOGGING to FULL to access all logs from supervisor. For example start your container with:
cker run -d -p 8080:80 -p 8021:21 -e "GALAXY_LOGGING=full" bgruening/galaxy-stable
In addition you can access the supersisord webinterface on port 9002 and get access to log files. Start your container with:
cker run -d -p 8080:80 -p 8021:21 -p 9002:9002 -e "GALAXY_LOGGING=full" bgruening/galaxy-stable
If your tools are already included in the Tool Shed, building your own personalised Galaxy docker Image (Galaxy flavour) can be done using the following steps:
DockerfileFROM bgruening/galaxy-stable at the top of the file. This means that you use the Galaxy Docker Image as base Image and build your own extensions on top of it.install_tool_shed_repositories.py script.docker build -t='my-docker-test'docker run -p 8080:80 my-docker-testhttp://localhost:8080For example have a look at the deepTools or the ChemicalToolBox Dockerfile's.
laxy - deepTools
RSION 0.2
bgruening/galaxy-stable
TAINER Björn A. Grüning, bjoern.gruening@gmail.com
GALAXY_CONFIG_BRAND deepTools
DIR /galaxy-central
stall deepTools
install-repository \
"--url https://toolshed.g2.bx.psu.edu/ -o bgruening --name deeptools"
rk folders as imported from the host.
ME ["/export/", "/data/", "/var/lib/docker"]
pose port 80 (webserver), 21 (FTP server), 8800 (Proxy)
SE :80
SE :21
SE :8800
tostart script that is invoked during container start
["/usr/bin/startup"]
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.
This repository uses a git submodule to include Ansible roles maintained by the Galaxy project.
You can clone this repository and the Ansible submodule with:
t clone --recursive https://github.com/bgruening/docker-galaxy-stable.git
Updating already existing submodules is possible with:
t submodule update --remote
You can file an github issue or ask us on the Galaxy development list.