recipe strmie-hd

Automated Huntington Disease polyQ pattern scanner.

Homepage:

https://github.com/mazzalab/STRmie-HD

Documentation:

https://mazzalab.github.io/STRmie-HD/

License:

MIT / MIT

Recipe:

/strmie-hd/meta.yaml

STRmie-HD (Short Tandem Repeat Mapping and Identification Engine - Huntington's Disease) is an interactive, Python-based tool designed to support the curation, visualization, and interpretation of short tandem repeat (STR) genotyping data obtained from Huntington's Disease (HD) patients. It enables the prediction, refinement and validation of CAG/CCG repeat expansion results in the context of HD, by highlighting cases of allelic instability or potential misclassification.

package strmie-hd

versions:

1.0.0-0

depends biopython:

depends colorama:

depends h5py:

depends jinja2:

depends joblib:

depends matplotlib-base:

depends numpy:

depends openpyxl:

depends pandas:

depends pytest:

depends python:

>=3.8

depends regex:

depends scikit-learn:

depends scipy:

depends seaborn:

depends xlrd:

requirements:

additional platforms:

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 strmie-hd

and update with::

   mamba update strmie-hd

To create a new environment, run:

mamba create --name myenvname strmie-hd

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/strmie-hd:<tag>

(see `strmie-hd/tags`_ for valid values for ``<tag>``)

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