iReceptor Gateway Turnkey

A "dockerized" iReceptor Gateway.

⚠️ It's an alpha version with the current limitations:

• long downloads will time out
• user pages (user list, user profile) are not working

System requirements

• Linux Ubuntu (tested on Ubuntu 16.04)
• sudo without password (often already enabled on virtual machines).

Note: this turnkey is a quick and easy way to get a gateway up and running on a VM running Linux Ubuntu. You could instead do the installation manually on a different system, by following the Docker files instructions and adapting them accordingly.

Installation

Download this repository

git clone https://github.com/sfu-ireceptor/turnkey-gateway.git

Create a TSV file with your list of users

Copy and edit the example file:

cd turnkey-gateway
cp data/users.tsv.example data/users.tsv

vi data/users.tsv 

Note: more users can be added later.

Execute the installation script.

Multiple Docker images will be downloaded from DockerHub, so this might take up to 30 min.

scripts/install_turnkey.sh

Check it's working

Replace "localhost" with your server URL if necessary:

curl localhost/login

The HTML code of the login page should be displayed.

Then go to that URL http://localhost/login in your browser and log as one of your previously defined users. Note: in this alpha version, the password is not actually verified.

Starting and stopping the Turnkey

scripts/start_turnkey.sh

scripts/stop_turnkey.sh

These scripts start and stop the Docker containers.

Adding more users

Edit data/users.tsv, then run:

scripts/load_users.sh

Note: existing users (with a username already in the database) will be updated, not duplicated.

Adding repositories

Your gateway comes preloaded with public AIRR repositories. To add more repositoires, create private_rest_services.tsv:

cp data/private_rest_services.tsv.example data/private_rest_services.tsv

Edit it (and remove the two examples it contains). Make sure your repositories URLs end with /airr/v1/ (don't forget the trailing slash!).

Then run:

scripts/load_private_repositories.sh

Note: existing repositories (with a URL already in the database) will be updated, not duplicated.

Your repositories will be enabled by default. Go to http://localhost/admin/databases (replace localhost by your server name).

Check your repositories are enabled, and for each one, refresh the cached sequence counts and max_size/stats. Also, at the bottom of the page, click "Refresh cached repertoire metadata". Then go to the repertoires page and check your repository data is displayed properly: http://localhost/samples

Other information

If something looks wrong

• Troubleshooting 🔨

Contact us

✉️ [email protected]