recipe mirnature

MiRNAture improves on ideas from MIRfix and integrates it with homology search. miRNAture is specifically designed to identify and annotate metazoan miRNAs in a homology-based setting and is complementary to tools and pipelines that extract miRNA candidates from small RNA-seq data

Homepage:

https://github.com/Bierinformatik/miRNAture

License:

GPL / GPL-3.0

Recipe:

/mirnature/meta.yaml

package mirnature

versions:

1.1-2,  1.1-1,  1.1-0,  1.0-5,  1.0-4,  1.0-3,  1.0-2,  1.0-1,  1.0-0

depends biopython:

>=1.78

depends blast:

>=2.13.0

depends clustalo:

>=1.2.4

depends hmmer:

>=3.3.2

depends infernal:

>=1.1.4

depends mirfix:

>=2.1.1

depends parallel:

>=20220922

depends perl:

>=5.32.1

depends perl:

>=5.32.1,<6.0a0 *_perl5

depends perl-bioperl:

>=1.6.924

depends perl-file-copy-recursive:

>=0.45

depends perl-io-string:

>=1.08

depends perl-io-stringy:

>=2.113

depends perl-module-build:

>=0.4224

depends perl-module-implementation:

>=0.09

depends perl-moose:

>=2.2201

depends perl-moosex-types-path-class:

>=0.09

depends perl-statistics-r:

>=0.34

depends perl-yaml-tiny:

>=1.73

depends pyfaidx:

>=0.7.1

depends python:

>3

depends r-base:

>=4.1.0

depends r-dplyr:

>=1.0.10

depends rmblast:

>=2.9.0

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 mirnature

and update with::

   mamba update mirnature

To create a new environment, run:

mamba create --name myenvname mirnature

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/mirnature:<tag>

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

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