This is the repository for the CCLE pipeline

This pipeline is considered End-to-End and will take you from downloading the raw data needed to a fully annotated dataset.

STATUS REPORT

Requirements & Setup

• Snakemake

Using Conda

!NOTE: This repo no longer uses conda in favor of pixi for package management. The conda environment file is still available for reference but not guaranteed to be up-to-date.

Ensure you have conda installed. If not, install miniconda. Install mamba for faster package management:

conda install mamba -n base -c conda-forge 

mamba env create -f workflow/envs/pipeline.yaml
conda activate ccle_snakemake
snakemake --version

Using Pixi

pixi install

This makes sure that the lock is synchronized and version controlled.

pixi run snakemake --dryrun

Enter into the environment

pixi shell

# Exit the environment using "exit"

Running the pipeline

snakemake --profile workflow/profiles/local --cores <NUMBER_OF_CORES>

snakemake --profile workflow/profiles/labserver

snakemake --profile workflow/profiles/gcp 

So far, the following has been implemented

Using pixi

Running a single pixi command will run all the below commands:

pixi run graphs

Rulegraph

snakemake --rulegraph | dot -Tsvg > resources/rulegraph.svg

Directed Acyclic Graph (DAG)

snakemake -F --dag | dot -Tsvg > resources/dag.svg

Filegraph

snakemake --filegraph | dot -Tsvg > resources/filegraph.svg