recipe shortstack

ShortStack: Comprehensive annotation and quantification of small RNA genes

Homepage:

https://github.com/MikeAxtell/ShortStack

License:

MIT / MIT

Recipe:

/shortstack/meta.yaml

package shortstack

versions:

4.1.1-0,  4.1.0-0,  4.0.4-1,  4.0.4-0,  4.0.3-0,  4.0.2-0,  4.0.1-0,  4.0.0-0,  3.8.5-4, 

4.1.1-0,  4.1.0-0,  4.0.4-1,  4.0.4-0,  4.0.3-0,  4.0.2-0,  4.0.1-0,  4.0.0-0,  3.8.5-4,  3.8.5-3,  3.8.5-2,  3.8.5-1,  3.8.5-0,  3.8.3-0,  3.6-1,  3.6-0

depends bedtools:

depends biopython:

depends bowtie:

>=1.3.1

depends cutadapt:

depends numpy:

depends python:

>=3.12.3

depends samtools:

>=1.20

depends shorttracks:

>=1.2

depends strucvis:

>=0.9

depends tqdm:

depends viennarna:

2.*

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 shortstack

and update with::

   mamba update shortstack

To create a new environment, run:

mamba create --name myenvname shortstack

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/shortstack:<tag>

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

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