- recipe maegatk
Mitochondrial Alteration Enrichment and Genome Analysis Toolkit.
- Homepage:
- Documentation:
- License:
MIT / MIT
- Recipe:
- Links:
Processing and quality control of mitochondrial genome variants from MAESTER data.
- package maegatk¶
- Versions:
0.2.0-2,0.2.0-1,0.2.0-0- Depends:
on bioconductor-genomicranges
on bioconductor-summarizedexperiment
on biopython
on bwa
on click
on fgbio-minimal
on freebayes
on openjdk
on optparse-pretty
on pulp
<2.8on pysam
on pytest
on python
>=3on r-base
on r-data.table
on r-dplyr
on r-matrix
on regex
on ruamel.yaml
0.16.12.*on samtools
on snakemake-minimal
<8
- 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 maegatk
to add into an existing workspace instead, run:
pixi add maegatk
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 maegatk
Alternatively, to install into a new environment, run:
conda create -n envname maegatk
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/maegatk:<tag>
(see maegatk/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:
[](http://bioconda.github.io/recipes/maegatk/README.html)
