recipe superstr

A lightweight, alignment-free utility for detecting repeat-containing reads in short-read WGS, WES and RNA-seq data.

Homepage:

https://github.com/bahlolab/superSTR

License:

GPL-2.0

Recipe:

/superstr/meta.yaml

package superstr

versions:

1.0.1-4,  1.0.1-3,  1.0.1-2,  1.0.1-1,  1.0.1-0,  1.0.0-0

depends arch-py:

>=4.15

depends htslib:

>=1.20,<1.22.0a0

depends libcurl:

>=8.8.0,<9.0a0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends libzlib:

>=1.2.13,<2.0a0

depends matplotlib-base:

>=3.4.1

depends mpmath:

>=1.2.1

depends numpy:

>=1.20.1

depends pandas:

>=1.2.2

depends python:

>=3.8.3

depends scipy:

>=1.6.1

depends seaborn:

>=0.11.1

depends statsmodels:

>=0.12.2

depends tqdm:

>=4.59

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 superstr

and update with::

   mamba update superstr

To create a new environment, run:

mamba create --name myenvname superstr

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/superstr:<tag>

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

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