v2.3.2

Fixed PyYAML installation issue

v2.3.1

• Use file metadata DB by default (--db file). If you see any DB connection timeout then switch back to in-memory DB with --db in-memory, then you will pass the error but call-caching will be disabled.

• Changed default file path for such file DB (--file-db): ${local_out_dir}/caper-db_[WDL_BASENAME]_[INPUT_JSON_BASENAME]. local_out_dir can be defined either in command line or conf file (~/.caper/default.conf).

• Can use a relative path in input JSON. If it still doesn't work. pip install autouri --upgrade

• Changed local file hashing strategy from path+modtime to xxh64 to prevent call-caching's cache miss due to the same text file with different modtime (e.g. modified by touch).

• Fixed filelock issue. Run pip install autouri --upgrade to make sure to have autouri>=0.4.4.

v2.2.3

• caper init makes a simpler configuration file ~/.caper/default.conf with less commented instruction and parameters;
• Made documentation simpler.

v2.2.2

• Upgraded Cromwell from 65 to 82.
• Fixed issues
  • Issue #177: SGE/PBS/LSF resource parameters were not correctly propagated to backend.conf.
  • Issue #180: GCS engine stanza is missing in backend.conf

v2.2.1

Fixed issue #177

• Some parameters in CLI (sge_resource_param, pbs_resource_param and lsf_resource_param) were not passed correctly to CaperRunner class constructor.

v2.2.0

Deprecated scg and sherlock backends.
Use slurm backend instead and follow instruction on Caper's conf ~/.caper/default.conf after caper init slurm.

New HPC feature

• Unified command caper hpc for all HPC backend types (slurm, sge, pbs and lsf).
• caper hpc submit WDL -i INPUT.json --leader-job-name GOOD_NAME_FOR_LEADER [--conda | --singularity]
• caper hpc list: shows all Caper leader jobs
• caper hpc abort JOB_ID: terminate a Caper leader job including child jobs

Default walltime for a leader job is 48 hours by default. Check Caper's conf ~/.caper/default.conf to change it.

v2.1.3

• Fixed pip install issues.
• Fixed GCP instance creation shell script (upgraded Ubuntu: 16.04 to 20.04).
• Fixed caper init issue for SGE clusters.

v2.1.2

Hotfix for the auto-troubleshooter. (stderr + '.background' error)

v2.1.1

Fixed sbatch stalling issue on slurm backend

• ENCODE-DCC/atac-seq-pipeline#346

Troubleshooter can show stderr.background (stderr from cluster engines)

v2.1.0

Fixed all Singularity/Conda issuess on HPC backends (slurm, sge, pbs and lsf)

• Fixes #149
• docker attribute in WDL task's runtime is now safely ignored for HPC backends
• Singularity directory binding issue (sharing soft-linked input/output files between tasks)

Makes a new Cromwell STDOUT file if it exists

• For example, if cromwell.out exists on CWD then cromwell.out.1 is created.