AIRR Knowledge toolkit
Setup the local source code.
git clone https://github.com/airr-knowledge/ak-tools.git
cd ak-tools
# init submodules
git submodule update --init --recursive
Use the docker container to have a consistent development environment.
docker build . -t airrknowledge/ak-tools: build container with local code.docker run -v $PWD:/work -it airrknowledge/ak-tools bash: run container shell with local code mounted at /work.
A list of related and useful tools that have been developed through the iReceptor project:
- ADC Monitoring: Active monitoring of performance of ADC repositories.
- ADC Search: Command line tools for searching the ADC via the ADC API.
- AIRR Spec Flatten: Python code that traveses the AIRR YAML spec and creates a TSV file with columns that describe each AIRR field. This is used extensively within the iReceptor suite of software and makes it "easy" to add/remove fields from the data model for both the Gateway and the Turnkey.
- AIRR to Cell: Code to transform AIRR Cell/GEX data to other formats such as 10X and h5ad, which are more widely supported than the AIRR formats in other tools.
- ADC CDR3 search: Code that takes a list of CDR3s (e.g. from IEDB or VDJdb) and searches the ADC for those CDR3s.
- MHC to AIRR: Utility to take a TSV file of subject level MHC and generate AIRR Repertoire Metadata JSON that is suitable for loading into the iReceptor Turnkey (using the update_metadata.sh script).
- ADC Ontology Check: Utility that checks a provided list of fields to see if they adhere to CURIE and appropriate ontology ID/labels. The tool reads in the AIRR Spec, processes the Ontology section to extract the ontology lookup, and then for each repertoire in a repository checks to see if the fields have correct ontology IDs and labels.
- Tapis 3 Tools: Set of tools that can be used from the command line to access the iReceptor Tapis 3 tenant.