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@leepc12 leepc12 released this 13 Jun 21:32
· 20 commits to master since this release
v2.2.0
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Learn about vigilant mode.

Upgrade Caper to >=2.2.0 for new HPC features.

$ pip install caper>=2.2.0 --upgrade

Conda environment name change:

  • encode-atac-seq-pipeline -> encd-atac
  • 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 atac.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
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