Please refer to the new Turnkey repository: https://github.com/sfu-ireceptor/turnkey-service-php
A quick and easy way to build your own AIRR-seq repository.
- a database
- a web application exposing that database through the iReceptor API
- a script to load data into the database
- some test data
Requires Ubuntu (tested on 16.04) and a user with sudo rights. First, get the source code:
git clone https://github.com/sfu-ireceptor/turnkey-service.git
Then launch the installation, which will take 15 min:
cd turnkey-service
scripts/install.sh
Query the web application with a POST request at /v2/samples to get the list of samples:
curl -X POST -H "Content-Type: application/x-www-form-urlencoded" "http://localhost:8080/v2/samples"
An empty array is returned because the database is empty.
[]
- load the "sample metadata" associated with a study that has generated sequence data.
- load the available sequence annotations (from imgt, mixcr, etc).
Load the database admin user credentials:
source scripts/export.sh
Load the samples:
dataloading-mongo/scripts/dataloader.py -v --sample -d $MONGODB_DB -u $MONGODB_SERVICE_USER -p $MONGODB_SERVICE_SECRET -f dataloading-mongo/data/test/imgt/imgt_sample.csv
Check it worked:
curl -X POST -H "Content-Type: application/x-www-form-urlencoded" "http://localhost:8080/v2/samples"
Add the sequence annotations (answer yes to the warning, it will then take a few minutes):
dataloading-mongo/scripts/dataloader.py -v --imgt -d $MONGODB_DB -u $MONGODB_SERVICE_USER -p $MONGODB_SERVICE_SECRET -f dataloading-mongo/data/test/imgt/imgt.zip
Check it worked:
curl -X POST -H "Content-Type: application/x-www-form-urlencoded" "http://localhost:8080/v2/sequences_summary"
To see all dataloading options:
dataloading-mongo/scripts/dataloader.py -h
Contact: [email protected]