ENCODE-DCC/chip-seq-pipeline2: v2.0.0

Upgrade Caper to the latest >=2.0.0. Old versions of Caper won't work correctly on HPCs.

$ pip install caper --upgrade
$ caper -v # check if >=2.0.0

Conda users must re-install pipeline's Conda environments. YOU DO NOT NEED TO ACTIVATE CONDA ENVIRONMENT BEFORE RUNNING A PIPELINE. New Caper internally runs each task inside an installed Conda environment.

$ bash scripts/uninstall_conda_env.sh
$ bash scripts/install_conda_env.sh

HPC USERS MUST SPECIFY AN ENVIRONMENT TO RUN A PIPELINE ON. Choices are --conda, --singularity and --docker. This pipeline defaults to run with --docker so it will not work on HPCs without caper run ... --conda or caper run ... --singularity. It's recommended to use Singularity if your cluster supports it.

Please read new Caper (>=2.0.0)'s README carefully. There are very important updates on Caper's side for better HPC (Conda/Singularity/SLURM/...) support.