recipe roary

Rapid large-scale prokaryote pan genome analysis

Homepage:

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

License:

GPL-3.0

Recipe:

/roary/meta.yaml

Links:

biotools: roary, usegalaxy-eu: roary

package roary

versions:

3.13.0-1,  3.13.0-0,  3.12.0-2,  3.12.0-1,  3.12.0-0,  3.10.2-0,  3.9.1-0,  3.8.2-0,  3.8.0-1, 

3.13.0-1,  3.13.0-0,  3.12.0-2,  3.12.0-1,  3.12.0-0,  3.10.2-0,  3.9.1-0,  3.8.2-0,  3.8.0-1,  3.7.0-0

depends bedtools:

depends blast:

depends cd-hit:

depends fasttree:

depends mafft:

depends mcl:

depends parallel:

>=20180522

depends perl:

>=5.26.2,<5.26.3.0a0

depends perl-array-utils:

depends perl-bioperl:

>=1.7.2

depends perl-digest-md5-file:

depends perl-exception-class:

depends perl-file-find-rule:

depends perl-file-grep:

depends perl-file-path:

depends perl-file-slurper:

depends perl-file-temp:

depends perl-file-which:

depends perl-getopt-long:

depends perl-graph:

depends perl-graph-readwrite:

depends perl-log-log4perl:

depends perl-moose:

depends perl-perlio-utf8_strict:

depends perl-text-csv:

depends prank:

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 roary

and update with::

   mamba update roary

To create a new environment, run:

mamba create --name myenvname roary

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/roary:<tag>

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

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