- 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 bioconductor-genomicranges:
- depends bioconductor-summarizedexperiment:
- depends biopython:
- depends bwa:
- depends click:
- depends fgbio-minimal:
- depends freebayes:
- depends openjdk:
- depends optparse-pretty:
- depends pulp:
<2.8- depends pysam:
- depends pytest:
- depends python:
>=3- depends r-base:
- depends r-data.table:
- depends r-dplyr:
- depends r-matrix:
- depends regex:
- depends ruamel.yaml:
0.16.12.*- depends samtools:
- depends snakemake-minimal:
<8- 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 maegatk and update with:: mamba update maegatk
To create a new environment, run:
mamba create --name myenvname maegatk
with
myenvnamebeing 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/maegatk:<tag> (see `maegatk/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
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