Closed leepc12 closed 2 years ago
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
$ scripts/uninstall_conda_env.sh $ scripts/install_conda_env.sh
Caper's new HPC feature
caper hpc
slurm
sge
pbs
lsf
~/.caper/default.conf
caper init YOUR_BACKEND
caper hpc submit chip.wdl -i INPUT.json --leader-job-name GOOD_NAME_FOR_LEADER [--conda | --singularity]
caper hpc list
caper hpc abort JOB_ID
Upgrade Caper to >=2.2.0 for new HPC features.
Conda environment name change:
encode-chip-seq-pipeline
->encd-chip
Caper's new HPC feature
caper hpc
for all HPC backend types (slurm
,sge
,pbs
andlsf
).~/.caper/default.conf
) and runcaper 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 jobscaper hpc abort JOB_ID
: terminate a Caper leader job including child jobs