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@leepc12 leepc12 released this 07 Nov 03:15
v0.6.0
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Learn about vigilant mode.

IMPORATNT: Caper defaults back to NOT use a file-based metadata DB, which means no call-caching (re-using outputs from previous workflows) by default.

IMPORATNT: Even if you still want to use a file-based DB (--db file and --file-db [DB_PATH]), metadata DB generated from Caper<0.6 (with Cromwell-42) is not compatible with metadata DB generated from Caper>=0.6 (with Cromwell-47). Refer to this doc for such migration.

See this for details about metadata DB. Define a DB type with db= in your conf ~/.caper/default.conf to use a metadata DB.

Engine update

  • Upgraded default crowmell JAR version: 42 -> 47
    • Some feature of Caper will only work with 47 (e.g. PostgreSQL support, some bug fixes).

Then how to choose a DB?

  • You can choose a DB type with --db (or db= in conf file ~/.caper/default.conf). Then define chosen DB's required parameters (nothing required for in-memory DB).
    • Choices: file (unstable), mysql (recommended), postgresql and in-memory (new default but no call-caching).
  • mysql is recommended. We provide shell scripts (run_mysql_server_docker.sh and run_mysql_server_singularity.sh) to run a MySQL server with docker/singularity (without root).
  • See details at "Metadata database" section on README.

New features

  • Support for PostgreSQL DB for call-caching (Cromwell >= 43)

Change of parameters

  • New:
    • --db: in-memory (default), file (unstable), mysql (recommended) or postgresql (experimental).
    • --mysql-db-name: (optional) cromwell by default
    • --postgresql-db-ip: localhost by default
    • --postgresql-db-port: 5432 by default
    • --postgresql-db-user: (optional) cromwell by default
    • --postgresql-db-password: (optional) cromwell by default
    • --postgresql-db-name: (optional) cromwell by default
  • Deprecated:
    • --no-file-db: File DB is disabled by default. Many users reported that a file DB is unstable.

Bug fixes

  • PAPI v10 error (preemption error) on Google Cloud.
  • Caper didn't run WDL without --docker on cloud backends (aws and gcp).
    • Some WDL has docker image definition in each task (runtime { docker : }). Users had to specify a dummy docker image --docker ubuntu:latest to bypass this error.
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