recipe gargammel

Tool for simulating ancient DNA datasets

Homepage:

https://github.com/grenaud/gargammel

License:

GPL-3.0-only

Recipe:

/gargammel/meta.yaml

gargammel is a set of programs aimed at simulating ancient DNA fragments. For ancient hominin samples our program can also simulate various levels of present-day human contamination and microbial contamination.

package gargammel

versions:

1.1.2-6,  1.1.2-5,  1.1.2-4,  1.1.2-3,  1.1.2-2,  1.1.2-1,  1.1.2-0

depends art:

depends gsl:

>=2.7,<2.8.0a0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends libzlib:

>=1.2.13,<1.3.0a0

depends openssl:

1.0.2n.*

depends perl:

depends samtools:

depends zlib:

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 gargammel

and update with::

   mamba update gargammel

To create a new environment, run:

mamba create --name myenvname gargammel

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/gargammel:<tag>

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

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