Package Recipe 'mitoz'

recipe mitoz

MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes

Homepage:: https://github.com/linzhi2013/MitoZ
License:: GPLv3
Recipe:: /mitoz/meta.yaml

package mitoz¶

Versions:

3.6-1, 3.6-0, 3.5-0, 3.4-1, 3.4-0, 3.3-1, 3.3-0, 3.2-0, 3.1-0,

3.6-1, 3.6-0, 3.5-0, 3.4-1, 3.4-0, 3.3-1, 3.3-0, 3.2-0, 3.1-0, 3.0-0

Depends:

on biopython
on blast
on bs4
on bwa
on circos 0.69.*
on coreutils
on ete3 >=3.1.2
on fastp
on hmmer 3.1b2.*
on html5lib
on infernal 1.1.1.*
on libgd
on megahit
on openjdk
on perl 5.32.*
on perl-app-cpanminus
on perl-bioperl
on perl-clone
on perl-config-general
on perl-encode-locale
on perl-list-moreutils
on perl-math-bezier
on perl-math-round
on perl-math-vecstat
on perl-params-validate
on perl-set-intspan
on perl-statistics-basic
on perl-statistics-descriptive
on pkgconfig
on python >=3.6,<3.9
on requests
on samtools
on seqkit
on spades >=3.15.4
on tbl2asn
on tiara
on wise2

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 mitoz

to add into an existing workspace instead, run:

pixi add mitoz

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 mitoz

Alternatively, to install into a new environment, run:

conda create -n envname mitoz

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/mitoz:<tag>

(see mitoz/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/mitoz/README.html)