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https://github.com/hexylena/hello-world-interactive-environment
Simple "Hello, World" for building Galaxy IEs.
https://github.com/hexylena/hello-world-interactive-environment
Last synced: 16 days ago
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Simple "Hello, World" for building Galaxy IEs.
- Host: GitHub
- URL: https://github.com/hexylena/hello-world-interactive-environment
- Owner: hexylena
- License: other
- Created: 2015-07-10T18:55:28.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2018-10-09T13:40:06.000Z (about 6 years ago)
- Last Synced: 2024-10-17T14:05:45.021Z (about 1 month ago)
- Language: Mako
- Size: 103 KB
- Stars: 3
- Watchers: 2
- Forks: 5
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
Hello, World Interactive Environment
====================================
"Hello, World" for building IEs
Usage
=====
* Build your own image and run it
[Docker](https://www.docker.com) is a pre-requirement for this project. You can build the container with:
```bash
$ docker build -t hello-ie .
```
The build process can take some time, but if finished you can run your container with:
```bash
$ docker run -i -t -p 8000:8000 hello-ie
```
* Next, follow the [directions](galaxy-conf/README.md) in the `./galaxy-conf/`
folder to get the HelloWorld IE installed
* Ensure that the dynamic proxy is available:
```bash
$ cd $GALAXY/lib/galaxy/web/proxy/js
$ npm install .
```
* Set the following configuration options in your `$GALAXY/config/galaxy.ini` file:
```ini
dynamic_proxy_manage=True
dynamic_proxy_session_map=database/session_map.sqlite
# Pick a free port here
dynamic_proxy_bind_port=8800
dynamic_proxy_bind_ip=0.0.0.0
# Enable verbose debugging of Galaxy-managed dynamic proxy.
dynamic_proxy_debug=True
```
Also make sure that:
```ini
interactive_environment_plugins_directory = config/plugins/interactive_environments
```
is set in the same file, pointing to the directory where you IEs are. Otherwise the IEs won't be loaded.
* At this point you should be able to launch Galaxy, upload a text dataset,
and click "Visualize" and "HelloWorld"
* Galaxy will launch the Interactive Environment in the background. As you can
see the container was launched with this command built for you:
```console
$ docker run --sig-proxy=true \
-d -P \
-e "API_KEY=1712364174a0ff79b34e9a78fee3ca1c" \
-e "CORS_ORIGIN=http://localhost" \
-e "CUSTOM=42" \
-e "DEBUG=false" \
-e "GALAXY_PASTER_PORT=8000" \
-e "GALAXY_URL=http://localhost/galaxy/" \
-e "GALAXY_WEB_PORT=8000" \
-e "HISTORY_ID=f2db41e1fa331b3e" \
-e "PROXY_PREFIX=/galaxy/gie_proxy" \
-e "REMOTE_HOST=127.0.0.1" \
-e "[email protected]" \
-v "/tmp:/import/" \
-v "./README.md:/import/file.dat:ro" \
hello-ie
```
* In the UI the container should load (with a nice spinner) and then you should see this image:
where file.txt contains the content of the file which was mounted through the /import/
Environment Variables
=====================
Several environment variables are available by default, per IE rough standards
Variable | Use
------------------- | ---
`API_KEY` | Galaxy API Key with which to interface with Galaxy
`CORS_ORIGIN` | If the notebook is proxied, this is the URL the end-user will see when trying to access a notebook
`DEBUG` | Enable debugging mode, mostly for developers
`PROXY_PREFIX` | Used in Galaxy Interactive Environments to ensure that the GIE is under the same cookie path as Galaxy.
`GALAXY_URL` | URL at which Galaxy is accessible
`GALAXY_WEB_PORT` | Port on which Galaxy is running, if applicable
`HISTORY_ID` | ID of current Galaxy History, used in easing the dataset upload/download process
`NOTEBOOK_PASSWORD` | Password with which to secure the RStudio login. The default username is `galaxy`
`REMOTE_HOST` | Unused
Authors
=======
* Bjoern Gruening
* Helena Rasche
History
=======
- v0.1: Initial public release
- v0.2: Updated to 15.10 standards
- v0.3: Remove broken flask-hello