- recipe genomesyn2
A Comparative Genomics Framework Integrating Synteny Visualization
- Homepage:
- License:
MIT
- Recipe:
GenomeSyn2 is a flexible and high-performance framework for comparative genomics visualization, synteny construction, and multi-genome feature analysis. It supports multiple alignment engines (MUMmer, minimap2, BLASTp, Diamond, MMseqs2) and provides rich downstream visualization modules.
- package genomesyn2¶
- Versions:
1.1.0-0,1.0.0-0- Depends:
on blast
on cairosvg
on diamond
on gffread
on minimap2
on mmseqs2
on mummer4
on perl
>=5.32on perl-bioperl-core
on perl-svg
on python
>=3.8on seqkit
- 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 genomesyn2
to add into an existing workspace instead, run:
pixi add genomesyn2
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 genomesyn2
Alternatively, to install into a new environment, run:
conda create -n envname genomesyn2
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/genomesyn2:<tag>
(see genomesyn2/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/genomesyn2/README.html)
