https://github.com/edinburgh-genome-foundry/cuba
🏖️ The EGF Collection of Useful Bio Apps - Web demos of EGF software
https://github.com/edinburgh-genome-foundry/cuba
django dna-assembly docker-compose sequence-design synthetic-biology vuejs web-development
Last synced: 5 months ago
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🏖️ The EGF Collection of Useful Bio Apps - Web demos of EGF software
- Host: GitHub
- URL: https://github.com/edinburgh-genome-foundry/cuba
- Owner: Edinburgh-Genome-Foundry
- License: mit
- Created: 2017-10-06T11:49:43.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2022-12-10T19:07:40.000Z (over 2 years ago)
- Last Synced: 2024-07-30T20:48:28.826Z (9 months ago)
- Topics: django, dna-assembly, docker-compose, sequence-design, synthetic-biology, vuejs, web-development
- Language: Vue
- Homepage: http://cuba.genomefoundry.org
- Size: 16.3 MB
- Stars: 19
- Watchers: 5
- Forks: 3
- Open Issues: 27
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
The EGF Collection of Useful Biological Apps
[](https://travis-ci.org/Edinburgh-Genome-Foundry/CUBA)
This repository contains the source code of [cuba.genomefoundry.org](https://cuba.genomefoundry.org/),
a website of the Edinburgh Genome Foundry enabling anyone to use some of the EGF's
biological software.
## How is it built?
CUBA is based on the [CAB](https://github.com/Edinburgh-Genome-Foundry/CAB)
boilerplate, making it easy to create new apps with a form in the frontend and
custom computations in the backend. It features job
queues (with progress feedback for the user), form widgets like file uploaders,
help buttons, and many more.
### Getting started
The next steps will download, install, and launch CUBA on your computer.
1. Install ``docker`` and ``docker-compose`` on your machine. This step depends
on your machine (Windows, Linux, MacOS) so you'll need to google it.
2. Download CUBA from Github:
```
git clone https://github.com/Edinburgh-Genome-Foundry/CUBA.git
```
3. Go to the root ``CUBA/`` directory (the one containing this README and the
``docker-compose.yml``) and launch your application in development mode. The
first time you try this, Docker will download and build a lot of things,
which may take several minutes. It will only take a few seconds the next
times you run this command.
```
docker-compose up
```
4. Go to your browser and type ``localhost`` or ``127.0.0.1`` in the address bar.
You should see the website appear. the console in which you launched
``docker-compose`` will keep printing logs of the different components
(django, vue) so you can keep track and debug.
### Creating a new app
The next steps will add a new app to the CUBA project.
1. Go to ``frontend/src/components/scenarios`` and create a new scenario view
with a form, for instance by duplicating the file
[ExampleScenario.vue](https://github.com/Edinburgh-Genome-Foundry/CUBA/blob/master/frontend/src/components/scenarios/ExampleScenario.vue).
2. Register your scenario in file ``scenarios.js`` (in the same folder)
by adding ``require('./ExampleScenario')`` under the category you want.
You should now see your new scenario in the home page and the menu of the
website.
3. Next we will add some backend computations to process the form and return a
result. First go to ``backend/app/views`` and create a new folder
on the model of [``/example_scenario``](https://github.com/Edinburgh-Genome-Foundry/CUBA/tree/master/backend/app/views/example_scenario).
4. Register the scenario in ``backend/app/views/__init__.py`` by adding
```
from .example_scenario import ExampleScenarioView
```
5. Register the URL by adding the following line at the end of
``backend/website/urls.py``:
```
url(r'^api/start/example_scenario$',
views.ExampleScenarioView.as_view()),
```
6. That's it. You now have a new app with frontend and backend !
### Deploying the website on the web
The next steps will put your website on the web. Note that many other deployment
workflows are possible.
1. Get a hosting server (for instance from Amazon Web Services or Digital Ocean).
Get the IP address of this server (for instance ``123.12.123.123`` but
it could be ``mydomain.com`` if you have registered this domain and pointed it
to your server).
2. Log into this server (``ssh [email protected]`` or ``ssh [email protected]``)
and install Docker and Docker-Compose (some Digital Ocean servers come with
these already installed).
3. From your computer, in the CUBA root directory, run the following command to
create a code repository on the distant server, and register that distant
repository under the name ``prodserver``
```
./init_remote_git.sh [email protected] CUBA prodserver
```
4. On the remote server, in the folder ``CUBA.git``, start the website in
production mode:
```
docker-compose -f docker-compose.yml -f docker-compose.prod.yml up --build -d
```
5. Wait some time and go in your browser at the address ``123.12.123.123``,
your website should be live !
Every time you want to update the website, from your computer in the CUBA root
directory run ``git push prodserver master``. You will need to rebuild the
containers on the server if you have modified the frontend or added dependencies
to the backend (we may simplify this later).
Licence
-------
CUBA is an open source software originally written by [Zulko](https://github.com/Zulko)
at the [Edinburgh Genome Foundry](http://genomefoundry.org/) and released on
[Github](https://github.com/Edinburgh-Genome-Foundry/CUBA) under the MIT licence
(Copyright 2017 Edinburgh Genome Foundry). Everyone is welcome to contribute!
More biology software ?
-----------------------
EGF Codon is powered by the [EGF Codons](https://edinburgh-genome-foundry.github.io/)
synthetic biology software suite for DNA design, manufacturing and validation.