recipe circlator

circlator: a tool to circularise genome assemblies

Homepage:

https://github.com/sanger-pathogens/circlator

License:

GPL / GNU General Public License v3 (GPLv3)

Recipe:

/circlator/meta.yaml

package circlator

versions:

1.5.5-3,  1.5.5-2,  1.5.5-1,  1.5.5-0,  1.5.2-1,  1.5.2-0,  1.5.1-0,  1.5.0-0,  1.4.0-0, 

1.5.5-3,  1.5.5-2,  1.5.5-1,  1.5.5-0,  1.5.2-1,  1.5.2-0,  1.5.1-0,  1.5.0-0,  1.4.0-0,  1.3.1-0,  1.3.0-0,  1.1.2-0

depends amos:

>=3.1.0

depends bio_assembly_refinement:

>=0.4.0

depends bwa:

depends canu:

>=1.8

depends mummer:

>=3.23

depends openpyxl:

depends prodigal:

depends pyfastaq:

>=3.12.1

depends pymummer:

>=0.9.0

depends pysam:

>=0.8.1

depends python:

>=3

depends samtools:

depends spades:

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 circlator

and update with::

   mamba update circlator

To create a new environment, run:

mamba create --name myenvname circlator

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/circlator:<tag>

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

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