Package Recipe 'mirnature'

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:

on biopython >=1.78
on blast >=2.13.0
on clustalo >=1.2.4
on hmmer >=3.3.2
on infernal >=1.1.4
on mirfix >=2.1.1
on parallel >=20220922
on perl >=5.32.1
on perl >=5.32.1,<6.0a0 *_perl5
on perl-bioperl >=1.6.924
on perl-file-copy-recursive >=0.45
on perl-io-string >=1.08
on perl-io-stringy >=2.113
on perl-module-build >=0.4224
on perl-module-implementation >=0.09
on perl-moose >=2.2201
on perl-moosex-types-path-class >=0.09
on perl-statistics-r >=0.34
on perl-yaml-tiny >=1.73
on pyfaidx >=0.7.1
on python >3
on r-base >=4.1.0
on r-dplyr >=1.0.10
on rmblast >=2.9.0
on viennarna >=2.4.15

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install mirnature

to add into an existing workspace instead, run:

pixi add mirnature

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install mirnature

Alternatively, to install into a new environment, run:

conda create -n envname mirnature

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/mirnature:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/mirnature/README.html)