recipe strling

STRling (pronounced like “sterling”) is a method to detect large STR expansions from short-read sequencing data.

Homepage:

https://github.com/quinlan-lab/STRling

License:

MIT

Recipe:

/strling/meta.yaml

package strling

versions:

0.5.2-1,  0.5.2-0,  0.5.1-4,  0.5.1-3,  0.5.1-2,  0.5.1-1,  0.5.1-0,  0.5.0-0,  0.4.2-1, 

0.5.2-1,  0.5.2-0,  0.5.1-4,  0.5.1-3,  0.5.1-2,  0.5.1-1,  0.5.1-0,  0.5.0-0,  0.4.2-1,  0.4.2-0,  0.4.1-1,  0.4.1-0,  0.4.0-0,  0.3.0-0,  0.2.1-0,  0.1.0-0

depends biopython:

depends bpipe:

depends htslib:

>=1.17,<1.22.0a0

depends libgcc-ng:

>=12

depends pandas:

depends pysam:

depends pytest:

depends pytest-runner:

depends python:

>=3.7

depends scikit-learn:

depends seaborn:

depends statsmodels:

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 strling

and update with::

   mamba update strling

To create a new environment, run:

mamba create --name myenvname strling

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/strling:<tag>

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

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