recipe irma

IRMA: Iterative Refinement Meta-Assembler for the robust assembly, variant calling, and phasing of highly variable RNA viruses.

Homepage:

https://wonder.cdc.gov/amd/flu/irma/

License:

GNU General Public License v3 or later (GPLv3+)

Recipe:

/irma/meta.yaml

package irma

versions:

1.2.0-0,  1.1.4-0,  1.0.3-0,  1.0.2-2,  1.0.2-1,  1.0.2-0

depends blat:

>=35

depends fasttree:

>=2.1.3

depends minimap2:

>=2.17

depends muscle:

>=3.8.1551

depends parallel:

>=20181022

depends perl:

>=5.32.1,<6.0a0 *_perl5

depends pigz:

>=2.3.4

depends r-base:

>=3.5.1

depends samtools:

>=1.2

depends zip:

>=3.0

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 irma

and update with::

   mamba update irma

To create a new environment, run:

mamba create --name myenvname irma

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/irma:<tag>

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

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Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/irma/README.html)