recipe pypgatk

The Pypgatk framework and library provides a set of tools to perform ProteoGenomics Analysis.

Homepage:

http://github.com/bigbio/py-pgatk

Documentation:

https://pgatk.readthedocs.io/en/latest/pypgatk.html

Developer docs:

https://github.com/bigbio/py-pgatk

License:

APACHE / Apache 2

Recipe:

/pypgatk/meta.yaml

package pypgatk

versions:

0.0.24-0,  0.0.23-0,  0.0.22-0,  0.0.19-0,  0.0.18-0,  0.0.17-0,  0.0.16-0,  0.0.15-0,  0.0.14-0, 

0.0.24-0,  0.0.23-0,  0.0.22-0,  0.0.19-0,  0.0.18-0,  0.0.17-0,  0.0.16-0,  0.0.15-0,  0.0.14-0,  0.0.13-0,  0.0.12-0,  0.0.11-0,  0.0.10-0,  0.0.9-0,  0.0.8-0,  0.0.4-0

depends biopython:

depends click:

depends gffutils:

depends numpy:

depends pandas:

depends pathos:

depends pyahocorasick:

depends pybedtools:

depends pyopenms:

2.7.0

depends pysam:

>=0.16

depends pyteomics:

>=4.2

depends python:

>=3

depends pyvcf:

depends pyyaml:

depends ratelimit:

depends requests:

depends simplejson:

depends tqdm:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install pypgatk

and update with::

   mamba update pypgatk

To create a new environment, run:

mamba create --name myenvname pypgatk

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/pypgatk:<tag>

(see `pypgatk/tags`_ for valid values for ``<tag>``)

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Link to this page

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