v2.0.0

[leepc12]

New Caper 2.0.0. is out.

There is no significant update for cloud-based backends (gcp and aws).
Most updates are for HPC USERS to fix various annoying Singularity/Conda and cluster (SLURM, ...) issues.

For HPC users

HPC users must initialize Caper's configuration file. This will add new important parameters and description/instruction for them. Please make a copy of your original configuration file (~/.caper/default.conf) and then initialize it with caper init.

$ cp ~/.caper/default.conf ~/.caper/default.conf.bak
$ caper init [YOUR_BACKEND]  # local, slurm, sge, pbs, lsf. See README.md for details

Follow instruction comments in the configuration file. Most parameters will be the same as those in the original configuration file.

For Conda/Singularity users on HPC

YOU DO NOT NEED TO ACTIVATE CONDA ENVIRONMENT BEFORE RUNNING PIPELINES. Just make sure that pipeline's Conda environment is correctly installed and add --conda to the command line caper run ... --conda. New Caper 2.0.0 runs each WDL task inside a Conda environment.

We strongly recommend to use Singularity for new ENCODE ATAC-seq and ChIP-seq pipelines (both >=v2.0.0). caper run ... --singularity if your cluster support Singularity.

Added resource parameters for HPC

Added a resource parameter for each HPC backend so that users can customize resource parameters for the job submission command line (squeue, qsub, ...) according to their cluster configuration. It will be appended to the job submission command line. WDL syntax is allowed in ${} notation. Please find details in the configuration file after initialization. See README for details.

• slurm backend: slurm-resource-param
• sge backend: sge-resource-param
• pbs backend: pbs-resource-param
• lsf backend: lsf-resource-param