recipe zga

Prokaryotic genome assembly and annotation pipeline

Homepage:

https://github.com/laxeye/zga

Developer docs:

https://github.com/laxeye/zga/

License:

BSD / BSD

Recipe:

/zga/meta.yaml

package zga

versions:

0.1.0-0,  0.0.9.post2-1,  0.0.9.post2-0,  0.0.9-0,  0.0.8-0,  0.0.7-0

depends bbmap:

depends biopython:

depends blast:

depends checkm-genome:

>=1.1.0

depends dfast:

>=1.2.12

depends fastp:

depends flye:

>=2.6

depends mash:

>=2

depends minimap2:

depends nxtrim:

depends python:

>=3.6

depends racon:

depends samtools:

>=1.9

depends spades:

>=3.12

depends unicycler:

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 zga

and update with::

   mamba update zga

To create a new environment, run:

mamba create --name myenvname zga

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/zga:<tag>

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

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