Basic usageΒΆ

Access first level modules:

$ pype
error: too few arguments
usage: pype [-p PROFILE] {snippets,profiles} ...

Slim and simple framework to ease the managements of data, tools and
pipelines in the computerome HPC

positional arguments:
    snippets        Snippets
    profiles        List of profiles

optional arguments:
  -p PROFILE, --profile PROFILE
                    Select profile to set reference genome and tools

This is version 0.0.1 - Francesco Favero - 7 March 2016

Access submodules in the selected level:

$ pype snippets
error: too few arguments
usage: pype snippets {test} ...

positional arguments:
    test  test_snippets

Execute or access submodule:

$ pype snippets test
error: argument --test is required
usage: pype snippets test --test TEST [-o OPT]

optional arguments:
  --test TEST  Test metavar
  -o OPT       test option
$ pype snippets test --test World
Hello World
$ pype snippets test --test mate -o Cheers
Cheers mate

It is possible to pass local folders where to pick custom snippets and profiles via environment variables:

$ PYPE_SNIPPETS="/path/to/custom_snippets" \
  PYPE_PROFILES="/path/to/custom_profiles" pype

Or alternatively it is possible to set custom PYPE_SNIPPETS and PYPE_PROFILES in the ~/.bashrc (or alternatives) file.