.. _`bio/open-cravat/module`:

OPENCRAVAT MODULE
=================


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/open-cravat/module?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/open-cravat/module

Install OpenCRAVAT modules. Annotate variant calls with OpenCRAVAT. For more details, see https://github.com/KarchinLab/open-cravat/wiki.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule opencravat_module:
        output:
            # add any other desired modules as separate directory outputs
            directory("modules/annotators/biogrid"),
        log:
            "logs/open-cravat/module.log"
        wrapper:
            "v3.0.1/bio/open-cravat/module"

Note that input, output and log file paths can be chosen freely.

When running with

.. code-block:: bash

    snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.


Software dependencies
---------------------

* ``open-cravat=2.4.1``




Authors
-------

* Rick Kim


Code
----

.. code-block:: python

    __author__ = "Rick Kim"
    __copyright__ = "Copyright 2020, Rick Kim"
    __license__ = "GPLv3"

    from snakemake.shell import shell
    import cravat
    import re
    import pathlib
    import os

    log = snakemake.log_fmt_shell(stdout=True, stderr=True)
    onames = []
    for o in snakemake.output:
        onames.append(o)
    if type(onames) == str:
        onames = [onames]
    elif type(onames) == list:
        onames = onames
    else:
        onames = [str(onames)]
    for oname in onames:
        if os.path.exists(oname):
            continue
        [o2, module_name] = os.path.split(oname)
        [modules_dir, module_type] = os.path.split(o2)
        module_type = module_type[:-1]
        modules_dir_cur = cravat.admin_util.get_modules_dir()
        if modules_dir_cur != modules_dir:
            cravat.admin_util.set_modules_dir(modules_dir)
        cmd = ["oc", "module", "install", module_name, "-y"]
        cmd = " ".join(cmd)
        shell("{cmd} {log}")


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