Merge pull request #49 from bgruening/dev

Release version 15.03 based on Galaxy 15.03

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "galaxy/roles/galaxyproject.galaxyextras"]
+	path = galaxy/roles/galaxyprojectdotorg.galaxyextras
+	url = https://github.com/galaxyproject/ansible-galaxy-extras

README.md

@@ -7,30 +7,38 @@ One of the main goals is to make the access to entire tool suites as easy as pos
 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 [Debian/wheezy](http://www.debian.org/). and all recommended Galaxy requirements are installed.
+The Image is based on [Ubuntu 14.04 LTS](http://releases.ubuntu.com/14.04/) and all recommended Galaxy requirements are installed. The following chart should illustrate the [Docker](http://www.docker.io) 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.
+
+![Docker hierarchy](chart.png)
 
 
 Usage
 =====
 
-At first you need to install docker. Please follow the instruction on https://www.docker.io/gettingstarted/#h_installation
+At first you need to install docker. Please follow the [very good instructions](https://docs.docker.com/installation/) from the Docker project.
 
 After the successful installation, all what you need to do is:
 
-``docker run -d -p 8080:80 -p 8021:21 bgruening/galaxy-stable``
+  ```sh
+  docker 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](http://docs.docker.io/), 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](https://index.docker.io/u/bgruening/galaxy-stable/). ``-d`` will start the docker container in daemon mode. For an interactive session, you can execute:
 
-``docker run -i -t -p 8080:80 bgruening/galaxy-stable /bin/bash``
+  ```sh
+  docker 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:
 
-``docker run -d -p 8080:80 -v /home/user/galaxy_storage/:/export/ bgruening/galaxy-stable``
+  ```sh
+  docker 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:
 
@@ -45,85 +53,163 @@ 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/ bgruening/galaxy-stable``
+  ```bash
+  docker 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.
 
 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
+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`
+
+  ```bash
+  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/ \
+    bgruening/galaxy-stable
+  ```
+
+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.
+
+  ```bash
+  docker run -p 8080:80 -e "NONUSE=reports" bgruening/galaxy-stable
+  ```
+
+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:
+
+  ```sh
+  GALAXY_CONFIG_ADMIN_USERS=admin@galaxy.org
+  GALAXY_CONFIG_MASTER_API_KEY=HSNiugRFvgT574F43jZ7N9F3
+  GALAXY_CONFIG_BRAND="Galaxy Docker Build"
+  ```
 
-``docker run -d -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``
+You can and should overwrite these during launching your container:
 
-Enabling the Galaxy Report Tool
--------------------------------
+  ```bash
+  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'" \
+    bgruening/galaxy-stable
+  ```
 
-For admins wishing to have more information on the status of a galaxy instance, you can start this image with ``-p 9001:9001`` to serve the Galaxy Report Tool 
-on port 9001 on your host system.
+Personalize your Galaxy
+-----------------------
 
-``docker run -d -p 8080:80 -p 8021:21 -p 9001:9001 -v /home/user/galaxy_storage/:/export/ bgruening/galaxy-stable``
+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](`https://github.com/bgruening/docker-galaxy-stable/blob/master/galaxy/welcome.html`)).
+
+
+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.
+
+  ```bash
+  docker 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.
 
 
 Restarting Galaxy
 -----------------
 
-If you want to restart Galaxy without restarting the entire Galaxy container we can use `docker exec` (docker > 1.3).
+If you want to restart Galaxy without restarting the entire Galaxy container you can use `docker exec` (docker > 1.3).
+
+  ```sh
+  docker exec <container name> supervisorctl restart galaxy:
+  ```
 
-```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:
 
+  ```sh
+  docker run -p 9002:9002 bgruening/galaxy-stable
+  ```
 
-Advanced logging
+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" bgruening/galaxy-stable``
+  ```sh
+  docker 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:
 
+  ```sh
+  docker run -d -p 8080:80 -p 8021:21 -p 9002:9002 -e "GALAXY_LOGGING=full" bgruening/galaxy-stable
+  ```
 
-Extending the docker Image
+Extending the Docker Image
 ==========================
 
-If you have your Tools already included in the Tool Shed, building your own personalised Galaxy docker Image can be done using the following steps:
+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:
 
  1. Create a file the name ``Dockerfile``
  2. Include ``FROM 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.
  3. Install your Tools from the Tool Shed via the ``install_tool_shed_repositories.py`` script.
  4. execute ``docker build -t='my-docker-test'``
- 5. run your container with ``docker run -d -p 8080:80 my-docker-test``
+ 5. run your container with ``docker run -p 8080:80 my-docker-test``
  6. open your web browser on ``http://localhost:8080``
 
 For example have a look at the [deepTools](http://deeptools.github.io/) or the [ChemicalToolBox](https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox) Dockerfile's.
-
-https://github.com/bgruening/docker-recipes/blob/master/galaxy-deeptools/Dockerfile
-https://github.com/bgruening/docker-recipes/blob/master/galaxy-chemicaltoolbox/Dockerfile
+ * https://github.com/bgruening/docker-recipes/blob/master/galaxy-deeptools/Dockerfile
+ * https://github.com/bgruening/docker-recipes/blob/master/galaxy-chemicaltoolbox/Dockerfile
 
 ```
 # Galaxy - deepTools
 #
-# VERSION       0.1
+# VERSION       0.2
 
 FROM bgruening/galaxy-stable
 
 MAINTAINER Björn A. Grüning, bjoern.gruening@gmail.com
 
+ENV GALAXY_CONFIG_BRAND deepTools
+
 WORKDIR /galaxy-central
-RUN service postgresql start && service apache2 start && ./run.sh --daemon && sleep 120 && python ./scripts/api/install_tool_shed_repositories.py --api admin -l http://localhost:8080 --url
 
-# Mark one folders as imported from the host.
-VOLUME ["/export/"]
+# Install deepTools
+RUN install-repository \
+    "--url https://toolshed.g2.bx.psu.edu/ -o bgruening --name deeptools"
 
-# Expose port 80 to the host
+# Mark folders as imported from the host.
+VOLUME ["/export/", "/data/", "/var/lib/docker"]
+
+# Expose port 80 (webserver), 21 (FTP server), 8800 (Proxy)
 EXPOSE :80
+EXPOSE :21
+EXPOSE :8800
 
 # Autostart script that is invoked during container start
 CMD ["/usr/bin/startup"]
 ```
 
+List of Galaxy flavours
+-----------------------
+
+ * [docker-galaxy-blast](https://github.com/bgruening/docker-galaxy-blast)
+ * [ChemicalToolBox](https://github.com/bgruening/docker-recipes/blob/master/galaxy-chemicaltoolbox)
+ * [ballaxy](https://github.com/anhi/docker-scripts/tree/master/ballaxy)
+ * [docker-galaxy-deeptools](https://github.com/bgruening/docker-recipes/blob/master/galaxy-deeptools)
+ * [docker-galaxyp](https://github.com/bgruening/docker-galaxyp)
+
 
 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 ;)).
@@ -132,16 +218,34 @@ If you want to create new users, please make sure to use the ``/export/`` volume
 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`.
+
+
+Development
+-----------
+
+This repository uses a git submodule to include [Ansible roles](https://github.com/galaxyproject/ansible-galaxy-extras) maintained by the Galaxy project.
+
+You can clone this repository and the Ansible submodule with:
+
+  ```sh
+  git clone --recursive https://github.com/bgruening/docker-galaxy-stable.git
+  ```
+
+Updating already existing submodules is possible with:
+
+  ```sh
+  git submodule update --remote
+  ```
 
 Requirements
-============
+------------
 
 - [docker](https://www.docker.io/gettingstarted/#h_installation)
 
 
-
 History
-=======
+-------
 
  - 0.1: Initial release!
    - with Apache2, PostgreSQL and Tool Shed integration
@@ -150,10 +254,15 @@ History
  - 0.3: Add Interactive Environments
    - IPython in docker in Galaxy in docker
    - advanged logging
+ - 0.4:
+   - base the image on toolshed/requirements with all required Galaxy dependencies
+   - use Ansible roles to build large parts of the image
+   - export the supervisord webinterface on port 9002
+   - enable Galaxy reports webapp
 
 
 Support & Bug Reports
-=====================
+---------------------
 
-You can file an issue here https://github.com/bgruening/docker-galaxy-stable/issues or ask
-us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev
+You can file an [github issue](https://github.com/bgruening/docker-galaxy-stable/issues) or ask
+us on the [Galaxy development list](http://lists.bx.psu.edu/listinfo/galaxy-dev).