recipe pyfaidx

pyfaidx: efficient pythonic random access to fasta subsequences

Homepage:

https://github.com/mdshw5/pyfaidx/

Documentation:

https://pythonhosted.org/pyfaidx/

License:

BSD / BSD License

Recipe:

/pyfaidx/meta.yaml

Links:

biotools: pyfaidx, doi: 10.7287/peerj.preprints.970v1

package pyfaidx

versions:

0.8.1.3-0,  0.8.1.2-0,  0.8.1.1-0,  0.8.0-0,  0.7.2.2-0,  0.7.2.1-1,  0.7.2.1-0,  0.7.1-0,  0.7.0-1, 

0.8.1.3-0,  0.8.1.2-0,  0.8.1.1-0,  0.8.0-0,  0.7.2.2-0,  0.7.2.1-1,  0.7.2.1-0,  0.7.1-0,  0.7.0-1,  0.7.0-0,  0.6.4-0,  0.6.3.1-1,  0.6.3.1-0,  0.6.2-0,  0.6.1-0,  0.6.0-0,  0.5.9.5-0,  0.5.9.4-0,  0.5.9.2-0,  0.5.9.1-1,  0.5.9.1-0,  0.5.9-1,  0.5.9-0,  0.5.8-1,  0.5.8-0,  0.5.7-0,  0.5.6-0,  0.5.5.2-1,  0.5.5.2-0,  0.5.4.1-0,  0.5.3-0,  0.5.1-0,  0.5.0-0,  0.4.9.2-0,  0.4.8.1-4,  0.4.8.1-3,  0.4.8.1-2,  0.4.8.1-0,  0.4.7.1-3,  0.4.7.1-2,  0.4.7.1-0,  0.4.4-0

depends biopython:

depends importlib-metadata:

depends packaging:

depends python:

>=3.7

depends pyvcf3:

depends setuptools:

depends six:

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 pyfaidx

and update with::

   mamba update pyfaidx

To create a new environment, run:

mamba create --name myenvname pyfaidx

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/pyfaidx:<tag>

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

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