MIP can download many program prerequisites automatically via the mip download application
mip download [PIPELINE]. Each pipeline has a yaml file where available references are specified (rd_dna, [rdrna]((https://github.com/Clinical-Genomics/MIP/blob/develop/templates/mip_download_rd_rna_config-1.0-.yaml)) and the API is described here.
To download the references using MIP, run:
$ mip download [PIPELINE] --reference_dir <reference_dir> --config <download_config>
This will submit SLURM jobs that automatically downloads all references specified in the config that is not already present in the reference directory.
For a full list of download options, run:
$ mip download [PIPELINE] --help
Open the download config corresponding to your pipeline and update or add a new
version_tag in the reference hash. Update the same version tag together with any metadata changes in the reference_feature hash, see the API for details. Run the same mip command as above to download your updated reference.
To include the changes in the analysis - add your reference to your mip config.yaml file where appropriate.