v0.3.16

• change of default parameters

  • db-timeout: 10000 to 30000 (ms)
  • java-heap-run: 2G to 2G
  • java-heap-server: 8G to 7G

• added a subcommand debug , which is identical to troubleshoot.

v0.3.15

• bug fix for db key error when --no-file-db or -n is given but --file-db or -d is defined
• update doc for sbatch command
  • added -export=ALL to sbatch command to respect all environment variables (e.g. Conda activated PATH)

v0.3.14

• added --db-timeout to give longer time for Cromwell to connect to DB.
  • to prevent db - Connection is not available error even when no Caper/Cromwell process is attached to the DB file
  • this error can happen when DB file is large
  • default: 10000 (ms)

v0.3.13

• upgrade google API from v1 to v2: to fix PAPI 10 error
• added --gcp-zones to specify GCP zones to provision worker instances
  • e.g. --gcp-zones us-central1-b,us-west1-b

v0.3.12

• Bug fix for v0.3.11 (typo :: in the code)

v0.3.11

BUGGY. DO NOT USE USE v0.3.12 INSTEAD

• to support Croo's "soft-linking" on cloud storages
  • see this for details.

v0.3.10

• bug fix for caper list (non-hashable list error)
• update doc for ENCODE workshop 2019 at Seattle
• caper metadata prints out Python dict object { } instead of list of dict [ { } ] objects when there is only one workflow matched by search condition. Otherwise It keeps printing out lists of objects.

v0.3.9

• use input JSON file's basename for string label (-s / --str-label) if that is not specified in the command line
• added -v / --version to show version

v0.3.8

• added short parameters -d for --file-db and -n for --no-file-db
• fixed bug for --use-netrc not working with submit command
• added Minimum required parameters section to default conf file so that users only need to edit small number of parameters in that section. for TL;DR users.
• cromwell.jar will be downloaded on ~/.caper/cromwell_jar/ instead of a directory specified with --tmp-dir

v0.3.7

• Default time runtime attribute for cluster engines (SGE/SLURM/PBS)
  • default = 24 hours