recipe yasma

Small RNA annotation suite

Homepage:

https://github.com/NateyJay/YASMA

License:

GPL-3.0-only

Recipe:

/yasma/meta.yaml

Links:

doi: 10.1016/j.csbj.2025.05.045

This is a fully integrated pipeline for analysis of small RNAs based on short-read sequence data, focused on its annotation tool (YASMA-tradeoff). This tool produces accurate sRNA annotations in diverse species and library qualities, built specifically for dealing with samples with higher noise.

package yasma

versions:

1.0.1-0

depends bowtie:

depends click:

depends click-option-group:

depends cutadapt:

depends levenshtein:

depends numpy:

depends pprintpp:

depends pybigwig:

depends pysam:

depends python:

>=3.12

depends sra-tools:

depends viennarna:

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 yasma

and update with::

   mamba update yasma

To create a new environment, run:

mamba create --name myenvname yasma

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/yasma:<tag>

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

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