recipe mirfix

MIRfix automatically curates miRNA datasets by improving alignments of their precursors, the consistency of the annotation of mature miR and miR* sequence, and the phylogenetic coverage. MIRfix produces alignments that are comparable across families and sets the stage for improved homology search as well as quantitative analyses.

Homepage:

https://github.com/Bierinformatik/MIRfix

License:

GPL / GPL-3.0

Recipe:

/mirfix/meta.yaml

package mirfix

versions:

2.1.1-0,  2.1.0-1,  2.1.0-0,  2.0.1-0,  2.0.0-1,  2.0.0-0,  1.0.1-0

depends biopython:

>=1.78

depends blast:

>=2.13.0

depends clustalw:

>=2.1

depends dialign2:

>=2.2.1

depends matplotlib-base:

>=3.3.1

depends natsort:

>=6.2.0

depends numpy:

>=1.19.1

depends pyfaidx:

>=0.7.1

depends python:

>=3

depends tk:

>=8.6.10

depends viennarna:

>=2.4.15

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 mirfix

and update with::

   mamba update mirfix

To create a new environment, run:

mamba create --name myenvname mirfix

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/mirfix:<tag>

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

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