NOTE: this repository is now updated at cmap/dockerized_mts
Dockerized version of the PRISM MTS pipeline. For use with Merino pipeline output or clue.io datasets.
To get the associated docker image run:
docker pull aboghoss/clue-mts
Example command to run the container (see docker_wrapper.sh):
bash docker_wrapper.sh -i <INPUT_DIR> -o <OUTPUT_DIR> -p <PROJECT_NAME>
Requires the following files in the input data folder:
- PR300 and PR500 Level 2 data (.gctx format)
- PR300 and PR500 cell_info (long table)
- PR300 and PR500 inst_info (long table)
- project_key (long table mapping compounds to projects)
All files other than the Level 2 data can be in any format readable by data.table::fread