recipe lr_gapcloser

Use long sequenced reads to close gaps in assemblies.

Homepage:

https://github.com/CAFS-bioinformatics/LR_Gapcloser

Documentation:

https://github.com/CAFS-bioinformatics/LR_Gapcloser/blob/master/README.md

License:

GPL3 / GPL-3.0-or-later

Recipe:

/lr_gapcloser/meta.yaml

Links:

biotools: lrgapcloser, doi: 10.1093/gigascience/giy157

package lr_gapcloser

versions:

1.0-0

depends bwa:

depends minimap2:

depends perl:

>=5.32.1,<6.0a0 *_perl5

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 lr_gapcloser

and update with::

   mamba update lr_gapcloser

To create a new environment, run:

mamba create --name myenvname lr_gapcloser

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/lr_gapcloser:<tag>

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

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