recipe mitgard

Mitochondrial Genome Assembly from RNA-seq Data.

Homepage:

https://github.com/pedronachtigall/MITGARD

License:

GPL3 / GPL-3.0-or-later

Recipe:

/mitgard/meta.yaml

Links:

https: :https:`//doi.org/10.1093/bib/bbaa429`

package mitgard

versions:

1.1-0,  1.0-1,  1.0-0

depends biopython:

depends blast:

depends bowtie2:

depends canu:

depends hifiasm:

depends minimap2:

depends python:

>=3.6

depends samtools:

depends spades:

3.13.1.*

depends trinity:

2.8.5.*

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 mitgard

and update with::

   mamba update mitgard

To create a new environment, run:

mamba create --name myenvname mitgard

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/mitgard:<tag>

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

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