recipe pseudo-it

Reference-based genome assembly with iterative mapping

Homepage:

https://github.com/goodest-goodlab/pseudo-it

License:

GPL / GNU GPLv3

Recipe:

/pseudo-it/meta.yaml

Reference-based genome assembly with iterative mapping

package pseudo-it

versions:

3.1.1-0,  3.1.0-0,  3.0.0-0

depends bcftools:

depends bedtools:

depends bwa:

depends gatk4:

depends picard:

depends python:

>=3.10

depends samtools:

depends sed:

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 pseudo-it

and update with::

   mamba update pseudo-it

To create a new environment, run:

mamba create --name myenvname pseudo-it

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/pseudo-it:<tag>

(see `pseudo-it/tags`_ for valid values for ``<tag>``)

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