- recipe roary
Rapid large-scale prokaryote pan genome analysis
- Homepage:
- License:
GPL-3.0
- Recipe:
- Links:
- 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:
on bedtools
on blast
on cd-hit
on fasttree
on mafft
on mcl
on parallel
>=20180522on perl
>=5.26.2,<5.26.3.0a0on perl-array-utils
on perl-bioperl
>=1.7.2on perl-digest-md5-file
on perl-exception-class
on perl-file-find-rule
on perl-file-grep
on perl-file-path
on perl-file-slurper
on perl-file-temp
on perl-file-which
on perl-getopt-long
on perl-graph
on perl-graph-readwrite
on perl-log-log4perl
on perl-moose
on perl-perlio-utf8_strict
on perl-text-csv
on prank
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install roary
to add into an existing workspace instead, run:
pixi add roary
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install roary
Alternatively, to install into a new environment, run:
conda create -n envname roary
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/roary:<tag>
(see roary/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/roary/README.html)
