- recipe cats-rb
Reference-based transcriptome assembly quality assessment tool.
- Homepage:
- Documentation:
- License:
MIT
- Recipe:
CATS-rb evaluates transcriptome assemblies using the reference genome of the corresponding species.
- package cats-rb¶
- Versions:
1.0.3-0,1.0.2-0,1.0.1-0,1.0.0-0- Depends:
on bash
on bioconductor-complexheatmap
on bioconductor-genomeinfodb
on bioconductor-genomicdistributions
on bioconductor-genomicranges
on coreutils
on gawk
on pandoc
on r-base
>=4.3,<4.4.0a0on r-data.table
on r-egg
on r-ggdist
on r-ggplot2
on r-ggvenndiagram
on r-igraph
on r-matrix
on r-rmarkdown
on r-upsetr
on sed
on spaln
>=3.0.0
- 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 cats-rb
to add into an existing workspace instead, run:
pixi add cats-rb
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 cats-rb
Alternatively, to install into a new environment, run:
conda create -n envname cats-rb
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/cats-rb:<tag>
(see cats-rb/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/cats-rb/README.html)
