recipe mapdamage2

mapDamage: tracking and quantifying damage patterns in ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.

Homepage:

https://github.com/ginolhac/mapDamage

Documentation:

https://ginolhac.github.io/mapDamage

License:

MIT / MIT

Recipe:

/mapdamage2/meta.yaml

Links:

biotools: mapdamage, doi: 10.1093/bioinformatics/btt193, doi: 10.1093/bioinformatics/btr347

package mapdamage2

(downloads) docker_mapdamage2

versions:
2.2.3-0,  2.2.2-0,  2.2.1-0,  2.2.0-0,  2.1.1-1,  2.1.1-0,  2.1.0-0,  2.0.9-0,  2.0.8-0, 

2.2.3-0,  2.2.2-0,  2.2.1-0,  2.2.0-0,  2.1.1-1,  2.1.1-0,  2.1.0-0,  2.0.9-0,  2.0.8-0,  2.0.6-2,  2.0.6-1,  2.0.6-0

depends libgcc:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends pysam:

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends r-base:

depends r-gam:

depends r-ggplot2:

>=2.1.0

depends r-inline:

depends r-rcpp:

depends r-rcppgsl:

depends seqtk:

requirements:

additional platforms:
linux-aarch64,  osx-arm64

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 mapdamage2

and update with::

   mamba update mapdamage2

To create a new environment, run:

mamba create --name myenvname mapdamage2

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/mapdamage2:<tag>

(see `mapdamage2/tags`_ for valid values for ``<tag>``)

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