- recipe kalamari
A curated database of completed assemblies with taxonomy IDs
- Homepage:
- Documentation:
- Developer docs:
- License:
MIT / MIT
- Recipe:
Kalamari is a curated database of assemblies and taxonomies. These assemblies are curated mainly for foodborne bacteria but have other taxa such as SARS-CoV-2 and Crytposporidium. Taxonomy has been modified from NCBI Taxonomy and has been minimalized to just what is needed here.
- package kalamari¶
- Versions:
5.8.3-1,5.8.3-0,5.8.2-0,5.8.0-0,5.7.2-0,5.7.1-0,5.7.0-0,5.6.3-0,5.6.2-0,5.8.3-1,5.8.3-0,5.8.2-0,5.8.0-0,5.7.2-0,5.7.1-0,5.7.0-0,5.6.3-0,5.6.2-0,5.6.1-0,5.6.0-2,5.6.0-0,5.5.0-0,5.4.1-1,5.4.1-0,5.4.0-0,5.3.3-0,5.3.2-0,5.2.1-0- Depends:
on entrez-direct
on perl
>=5.32.1,<6.0a0 *_perl5on perl-module-build
- 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 kalamari
to add into an existing workspace instead, run:
pixi add kalamari
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 kalamari
Alternatively, to install into a new environment, run:
conda create -n envname kalamari
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/kalamari:<tag>
(see kalamari/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/kalamari/README.html)
