recipe amira

A tool to detect acquired AMR genes directly from long read sequencing data.

Homepage:

https://github.com/Danderson123/Amira

Documentation:

https://github.com/Danderson123/Amira/blob/main/README.md

License:

APACHE / Apache-2.0

Recipe:

/amira/meta.yaml

package amira

versions:

0.9.3-0,  0.9.2-0,  0.9.1-0

depends joblib:

1.2.0

depends kmer-jellyfish:

2.3.0

depends matplotlib-base:

3.6.2

depends minimap2:

2.17

depends numpy:

1.26.4

depends pandas:

2.2.2

depends pyfastaq:

3.17.0

depends pysam:

0.22.0

depends pytest:

7.2.0

depends python:

3.10

depends racon:

1.4.10

depends samtools:

1.18

depends scipy:

1.12.0

depends sourmash:

4.8.4

depends suffix-tree:

0.1.2

depends tqdm:

4.67.1

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 amira

and update with::

   mamba update amira

To create a new environment, run:

mamba create --name myenvname amira

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/amira:<tag>

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

Download stats

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/amira/README.html)