https://github.com/gdamaskos/flask_with_ajax_and_matrix_visualization
CCD is a web application that facilitates protein crystallography experiments. In this repository you can find the core of the application.
https://github.com/gdamaskos/flask_with_ajax_and_matrix_visualization
ajax bioinformatics bootstrap ccs crystallography flask google-material-design gunicorn html5 javascript jquery protein
Last synced: about 2 months ago
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CCD is a web application that facilitates protein crystallography experiments. In this repository you can find the core of the application.
- Host: GitHub
- URL: https://github.com/gdamaskos/flask_with_ajax_and_matrix_visualization
- Owner: gdamaskos
- Created: 2021-04-01T09:47:50.000Z (about 4 years ago)
- Default Branch: master
- Last Pushed: 2021-07-01T14:08:08.000Z (almost 4 years ago)
- Last Synced: 2023-11-23T14:33:40.318Z (over 1 year ago)
- Topics: ajax, bioinformatics, bootstrap, ccs, crystallography, flask, google-material-design, gunicorn, html5, javascript, jquery, protein
- Language: Python
- Homepage: https://ccd.rhpc.nki.nl
- Size: 6.34 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# CCD
CCD stands for Crystallisation Construct Designer.
CCD is a web application that facilitates protein crystallography experiments. In this repository you can find the core of the application.
You can visit the complete site https://ccd.rhpc.nki.nl
Basic web software used in this project:
* Flask
* JQuery
* AJAX
* Google Material Design
* Bootstrap
# Docker image run
If you do not have Docker you can install it in Ubuntu following these steps:
https://docs.docker.com/engine/install/ubuntu/
You can run the Docker image from the Docker Hub like this:
docker run -d -p 8888:5000 --name ccd_container gdamaskos/ccdimg
Then visit the address:
http://localhost:8888
Enjoy!
You can also find the Dockerfile in this repository's root directory.
# Installation for development on your computer
## Prerequisites
First of all, you must be running a Debian Operating System like Ubuntu.
The following prerequisites are required by CCD and must be installed manually if not present:
* predator (already uploaded in this repository's deps directory)
* uipred (already uploaded in this repository's deps directory)
* ncoils (e.g. `apt-get install ncoils` on a Debian-like OS)
* muscle (e.g. `apt-get install muscle` on a Debian-like OS)
* git (e.g. `apt-get install git` on a Debian-like OS)
* python 3.8, follow this tutorial to prepare https://www.digitalocean.com/community/tutorials/how-to-install-python-3-and-set-up-a-programming-environment-on-ubuntu-20-04-quickstart
## Steps for setting up the development environment
Clone the repository from github and go to the ccd directory:
git clone https://github.com/gdamaskos/flask_with_ajax_and_matrix_visualization.git
cd flask_with_ajax_and_matrix_visualization
Create a python3.8 virtual environment containing the dependences found in requirements.txt:
python3 -m venv ~/virtual_environments/ccd3
source ~/virtual_environments/ccd3/bin/activate
Install python dependencies:
pip install wheel
pip install -r requirements.txt
Modify the settings in `config/settings.example` to your needs and rename the
file to `config/ccd_settings.cfg`. Make sure you generate a new secret key,
and fill in a valid email to allow Uniprot to notify you in case of
problems.
The secret key can be generated using a python shell, for example:
$ python
>>> import os
>>> os.urandom(96)
Run the tests
./test.sh
Start the app!
./run_autoreload.sh
Visit the address:
http://localhost:5000
# Further options for deployment
If you would like to create `systemd` services to run CCD automatically see the `config/celery.service` and `config.ccd3.service`.
As an alternative, you can use python `supervisor` and use the `config/supervisor.conf` to make a system service ccd managed by supervisor (edit where necessary).
If you need to configure a reverse proxy with apache check `config/xxx-ccd.conf` to see an example.
The contact page (available only on developer versions for ccd.rhpc.nki.nl) requires a working Google maps API.
(see https://developers.google.com/maps/api-key-best-practices for how to obtain and configure one)
In short:
1. Generate an API key
2. Restrict it by HTML referrer to the website you are running CCD from + /contact (e.g. ccd.rhpc.nki.nl/contact)
3. Enable "Map Javascript API".
4. Add your API key to contact.html template in the place of the current key.