recipe mitosalt

MitoSAlt is a pipeline to identify large deletions and duplications in human and mouse mitochondrial genomes from next generation whole genome/exome sequencing data. The pipeline is capable of analyzing any circular genome in principle, as long as a proper configuration file is provided.

Homepage:

https://sourceforge.net/projects/mitosalt/

License:

MIT / MIT-0

Recipe:

/mitosalt/meta.yaml

This mitosalt version can:

- download user-selected reference genomes

- `download-mitosalt-db.sh -h [human_genome_url, blank for custom hg19 genome]` - `download-mitosalt-db.sh -m [mouse_genome_url, blank for custom GRCm38.p6 genome]` - `download-mitosalt-db.sh -h [human_genome_url, blank for custom hg19 genome] -m [mouse_genome_url, blank for custom GRCm38.p6 genome]`

- let us choose the destination folder of the reference genomes and indices

- `export MITOSALTDATA=/path/to/mitosalt/genomedata`

- specify custom config files that are available in the package at `$CONDA_PREFIX/share/mitosalt-1.1.1-0/`

package mitosalt

(downloads) docker_mitosalt

versions:

1.1.1-0

depends bedtools:

2.31.1.*

depends bioconductor-biostrings:

2.70.1.*

depends last:

1608.*

depends openjdk:

>=11.0.1

depends perl:

5.32.*

depends r-base:

4.3.3.*

depends r-plotrix:

3.8_4.*

depends r-rcolorbrewer:

1.1.*

depends samtools:

1.21.*

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 mitosalt

and update with::

   mamba update mitosalt

To create a new environment, run:

mamba create --name myenvname mitosalt

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/mitosalt:<tag>

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

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Link to this page

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