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DEVELOPMENT.md

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Notes on developing and debugging cactus

Overriding make settings

A file include.local.mk can be created in the root directory to override make variables, including setting environment variables. This should not be committed.

Environment variables controlling how cactus is run

  • CACTUS_BINARIES_MODE - how are cactus programs found?
    • docker
    • singularity
    • local
  • CACTUS_DOCKER_MODE - is Docker being used?
    • 1
    • 0
  • CACTUS_USE_LOCAL_IMAGE - is Docker image on local server?
    • 0
    • 1

Environment variables controlling tests

  • SON_TRACE_DATASETS location of test data set, currently available with git clone https://github.com/ComparativeGenomicsToolkit/cactusTestData

  • SONLIB_TEST_LENGTH filters tests by maximum run time length category (case-insensitive)

    • SHORT - tests taking less than ~10 seconds, with some exceptions
    • MEDIUM - tests taking less than ~100 seconds
    • LONG - test taking less than ~1000 seconds
    • VERG_LONG - test taking even longer

  • CACTUS_TEST_LOG_LEVEL - Set log-level used for the test, may not set it for all test, but very useful for Toil.

Running tests with docker in single machine mode

make docker
export CACTUS_USE_LOCAL_IMAGE=1
make test

Debugging hints

  • The main Cactus Python process will print out a stack trace of all of the Python threads if sent a SIGUSR1 signal. They will then continue execution. This maybe useful in determining the state of cactus.