Available modules:

Browse and install available modules

There are available set of snippets and pipelines. You can access the list of repository and manage the installed modules with the repos sub command

$ pype repos
usage: pype repos [-r REPO_LIST] {list,install,init,clean,info} ...

positional arguments:
  {list,install,init,clean,info}
    list                List the available repositories
    install             Install modules from selected repository
    init                Initiate an empty repository
    clean               Cleanup all module folders
    info                Print location of the modules currently in use

optional arguments:
  -r REPO_LIST, --repo REPO_LIST
                        Repository list. Default:
                        /home/docs/checkouts/readthedocs.org/user_builds/bio-
                        pype/envs/latest/lib/python3.7/site-packages/bio_pype-
                        1.9.99-py3.7.egg/pype/pype_modules/repos.yaml

The currently available sets are:

$ pype repos list
- gatk4
	Pype modules following the gatk4 best practice
	homepage: https://bitbucket.org/ffavero/pype_modules
	source: https://bitbucket.org/ffavero/pype_modules/get/master.tar.gz
- sequenza
	Pype modules to run sequenza
	homepage: https://bitbucket.org/sequenzatools/sequenza_pype_modules
	source: https://bitbucket.org/sequenzatools/sequenza_pype_modules/get/master.tar.gz
- weischenfeldt
	Pype modules for the Weischenfeldt group tools in computerome
	homepage: https://bitbucket.org/weischenfeldt/pype_weischenfeldt_computerome
	source: https://bitbucket.org/weischenfeldt/pype_weischenfeldt_computerome/get/master.tar.gz

It’s possible to install the modules from a repository in the list, by invoking the pype repos install with the selected repository.