recipe pharokka

Fast Phage Annotation Program

Homepage:

https://github.com/gbouras13/pharokka

Documentation:

https://pharokka.readthedocs.io

License:

MIT / MIT

Recipe:

/pharokka/meta.yaml

package pharokka

versions:

1.7.3-0,  1.7.2-0,  1.7.1-0,  1.7.0-0,  1.6.1-1,  1.6.1-0,  1.6.0-0,  1.5.1-0,  1.5.0-0, 

1.7.3-0,  1.7.2-0,  1.7.1-0,  1.7.0-0,  1.6.1-1,  1.6.1-0,  1.6.0-0,  1.5.1-0,  1.5.0-0,  1.4.1-0,  1.4.0-0,  1.3.2-0,  1.3.1-0,  1.3.0-1,  1.3.0-0,  1.2.1-0,  1.2.0-0,  1.1.0-0,  1.0.1-0,  1.0.0-0,  0.1.11-0,  0.1.10-0,  0.1.9-0,  0.1.8-0,  0.1.7-0,  0.1.6-0

depends alive-progress:

>=3.0.1

depends aragorn:

>=1.2.41

depends bcbio-gff:

>=0.7.0

depends biopython:

>=1.80,<1.82

depends black:

>=22.3.0

depends dnaapler:

>=0.4.0

depends isort:

>=5.10.1

depends loguru:

>=0.5.4

depends mash:

>=2.2

depends minced:

>=0.4.2

depends mmseqs2:

13.45111

depends phanotate:

>=1.5.0,<1.6.4

depends pycirclize:

>=0.3.1

depends pyhmmer:

>=0.10.0

depends pyrodigal:

>=3.1.0

depends pyrodigal-gv:

>=0.2.0

depends pytest:

>=6.2.5

depends pytest-cov:

>=3.0.0

depends python:

>=3.5

depends pyyaml:

>=6.0

depends requests:

>=2.25.1

depends trnascan-se:

>=2.0.9

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 pharokka

and update with::

   mamba update pharokka

To create a new environment, run:

mamba create --name myenvname pharokka

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/pharokka:<tag>

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

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