recipe pomoxis

Assembly, consensensus, and analysis tools by ONT research

Homepage:

https://github.com/nanoporetech/pomoxis

Documentation:

https://nanoporetech.github.io/pomoxis/index.html

License:

OTHER / MPL-2.0

Recipe:

/pomoxis/meta.yaml

package pomoxis

versions:

0.3.15-0,  0.3.13-0,  0.3.12-0,  0.3.11-0,  0.3.10-0,  0.3.9-0,  0.3.8-0,  0.3.7-0,  0.3.6-0, 

0.3.15-0,  0.3.13-0,  0.3.12-0,  0.3.11-0,  0.3.10-0,  0.3.9-0,  0.3.8-0,  0.3.7-0,  0.3.6-0,  0.3.5-1,  0.3.5-0,  0.3.4-0,  0.3.2-1,  0.3.2-0,  0.3.1-1,  0.3.1-0,  0.3.0-0,  0.2.5-0,  0.2.4-0,  0.2.3-0,  0.2.2-0

depends bcftools:

>=1.9

depends bedtools:

>=2.29.0

depends biopython:

>=1.63

depends intervaltree:

>=3

depends matplotlib-base:

>=3.2.1

depends miniasm:

>=0.3_r179

depends minimap2:

>=2.17

depends ncls:

>=0.0.65

depends numpy:

>=1.16.1

depends pandas:

>=0.24.2

depends porechop:

depends pysam:

>=0.15.2

depends python:

>=3.6

depends racon:

>=1.3.1

depends samtools:

>=1.9

depends seqkit:

>=0.8.0

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 pomoxis

and update with::

   mamba update pomoxis

To create a new environment, run:

mamba create --name myenvname pomoxis

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/pomoxis:<tag>

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

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