recipe pirate

Pangenome analysis and threshold evaluation toolbox

Homepage:

https://github.com/SionBayliss/PIRATE

License:

GPL / GPL3

Recipe:

/pirate/meta.yaml

Links:

biotools: pirate, doi: 10.1101/598391

package pirate

versions:

1.0.5-0,  1.0.4-2,  1.0.4-1,  1.0.4-0,  1.0.3-2,  1.0.3-1,  1.0.3-0,  1.0.2-1,  1.0.2-0

depends blast:

>=2.2.31

depends cd-hit:

>=4.7

depends diamond:

>=0.9.14

depends fasttree:

>=2.1.10

depends mafft:

>=7.310

depends mcl:

>=14.137

depends parallel:

>=20170422

depends perl-bioperl:

>=1.7.2

depends r-dplyr:

depends r-ggplot2:

depends unzip:

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 pirate

and update with::

   mamba update pirate

To create a new environment, run:

mamba create --name myenvname pirate

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/pirate:<tag>

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

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