Thanks for checking out TCRtoolkit-Bulk, the platform for bulk T Cell Repertoire analysis! TCRtoolkit-Bulk is wrapped in NextFlow, written in python, and uses Docker to manage dependencies.
We currently support bulk TCRseq data from Adaptive Biotechnologies.
- Nextflow
Nextflow can be used on any POSIX-compatible system (Linux, OS X, WSL). It requires Bash 3.2 (or later) and Java 11 (or later, up to 18) to be installed.
wget -qO- https://get.nextflow.io | bash
chmod +x nextflow
The nextflow executable is now available to run on the command line. The executable can be moved to a directory in your $PATH variable so you can run it from any directory.
- Docker
TCRtoolkit-Bulk runs in Docker containers available here. Depending on what operating system you are running (Linux, MacOS, WSL), please refer to the Docker documentation for installation instructions.
- TCRtoolkit-Bulk
git clone https://github.com/KarchinLab/TCRtoolkit-Bulk.git
cd TCRtoolkit-Bulk
Below is a minimal example of how to run the pipeline. The minimal-example dataset provided is a small subset of the dataset from this manuscript by Tumeh and Ribas et al. (2014). Note that the results are simply for demonstration purposes and are not intended for biological interpretation.
## from the TCRtoolkit-Bulk directory
nextflow run main.nf -entry bulk -c configs/bulk.config \
--samplesheet test_data/minimal-example/samplesheet.csv \
--data_dir test_data/minimal-example/ \
--output results/minimal-example