.. _`bio/genomepy`:

GENOMEPY
========


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

Download genomes the easy way:
https://github.com/vanheeringen-lab/genomepy



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule genomepy:
        output:
            multiext(
                "{assembly}/{assembly}",
                ".fa",
                ".fa.fai",
                ".fa.sizes",
                ".gaps.bed",
                ".annotation.gtf",
                ".blacklist.bed",
            ),
        log:
            "logs/genomepy_{assembly}.log",
        params:
            provider="ucsc",  # optional, defaults to ucsc. Choose from ucsc, ensembl, and ncbi
        cache: "omit-software"  # mark as eligible for between workflow caching
        wrapper:
            "v3.0.1/bio/genomepy"

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
---------------------

* ``genomepy=0.16.1``



Params
------

* ``provider``: which provider to download from, defaults to UCSC (choose from UCSC, Ensembl, NCBI).




Authors
-------

* Maarten van der Sande


Code
----

.. code-block:: python

    __author__ = "Maarten van der Sande"
    __copyright__ = "Copyright 2020, Maarten van der Sande"
    __email__ = "M.vanderSande@science.ru.nl"
    __license__ = "MIT"


    from snakemake.shell import shell

    # Optional parameters
    provider = snakemake.params.get("provider", "ucsc").lower()

    # set options for plugins
    all_plugins = "blacklist,bowtie2,bwa,gmap,hisat2,minimap2,star"
    req_plugins = ","
    if any(["blacklist" in out for out in snakemake.output]):
        req_plugins = "blacklist,"

    annotation = ""
    if any(["annotation" in out for out in snakemake.output]):
        annotation = "--annotation"

    # parse the genome dir
    genome_dir = "./"
    if snakemake.output[0].count("/") > 1:
        genome_dir = "/".join(snakemake.output[0].split("/")[:-1])

    log = snakemake.log

    # Finally execute genomepy
    shell(
        """
        # set a trap so we can reset to original user's settings
        active_plugins=$(genomepy config show | grep -Po '(?<=- ).*' | paste -s -d, -) || echo ""
        trap "genomepy plugin disable {{{all_plugins}}} >> {log} 2>&1;\
              genomepy plugin enable {{$active_plugins,}} >> {log} 2>&1" EXIT

        # disable all, then enable the ones we need
        genomepy plugin disable {{{all_plugins}}} >  {log} 2>&1
        genomepy plugin enable  {{{req_plugins}}} >> {log} 2>&1

        # install the genome
        genomepy install {snakemake.wildcards.assembly} \
        --provider {provider} {annotation} -g {genome_dir} >> {log} 2>&1
        """
    )


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