ENCODE-DCC/chip-seq-pipeline2: v2.2.0

Upgrade Caper to >=2.2.0 for new HPC features.

$ pip install caper>=2.2.0 --upgrade

Conda environment name change:

• encode-chip-seq-pipeline -> encd-chip
• Please reinstall your Conda environment after updating pipeline's git repo.

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

Caper's new HPC feature

• Unified command caper hpc for all HPC backend types (slurm, sge, pbs and lsf).
• Read Caper's README carefully and make a backup of your Caper's conf file (~/.caper/default.conf) and run caper init YOUR_BACKEND.
• caper hpc submit chip.wdl -i INPUT.json --leader-job-name GOOD_NAME_FOR_LEADER [--conda | --singularity]: submits a workflow to HPC's job engine.
• caper hpc list: shows all Caper leader jobs
• caper hpc abort JOB_ID: terminate a Caper leader job including child jobs