AIRR Knowledge extract, transform, validate, load pipeline
https://airr-knowledge.github.com/ak-etvl
The integration pipeline is in beta release and designed to be run within a docker container bash shell with host mounts to access data files.
This repository contains submodules. When doing a git clone, those submodules are
not automatically populated, and an additional command is required.
git clone https://airr-knowledge.github.com/ak-etvl
cd ak-etvl
git submodule update --init --recursive
Make a docker image from the local code:
make docker: builds docker image
Build custom image or pull published images:
docker build . -t airrknowledge/ak-schema:mytag: build container with local code with custom tag.docker pull airrknowledge/ak-schema:tag: pull published container for specific tagged version.docker pull airrknowledge/ak-schema: pull published container with latest code.
Within the docker container, run the etvl scripts
make iedb_tcrmake adc_chain