recipe pypolca

Standalone Python re-implementation of the POLCA polisher from MaSuRCA

Homepage:

https://github.com/gbouras13/pypolca

License:

MIT / MIT

Recipe:

/pypolca/meta.yaml

package pypolca

versions:

0.3.1-0,  0.3.0-0,  0.2.1-0,  0.2.0-0,  0.1.1-0

depends biopython:

>=1.76

depends bwa:

>=0.7.17

depends click:

>=8.0.0

depends freebayes:

>=1.3.1,<1.3.7

depends loguru:

>=0.5.3

depends pandas:

>=1.4.2

depends python:

>=3.8,<4.0

depends pyyaml:

>=6.0

depends samtools:

>=1.18

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 pypolca

and update with::

   mamba update pypolca

To create a new environment, run:

mamba create --name myenvname pypolca

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/pypolca:<tag>

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

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