- recipe colombo
A software framework equipped with a GUI for the prediction of genomic islands (GIs) in prokaryotes.
- Homepage:
- License:
Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
- Recipe:
COLOMBO is a software framework equipped with a GUI for the prediction of genomic islands (GIs) in prokaryotes. It can be equipped with different plugins that actually perform the prediction. The current version of COLOMBO is supplied with
SIGI-HMM that uses hidden Markov models and codon usage bias;
SIGi-CRF utilizing conditional random fields and tetramer-based order-3 Markov chain transition probabilities. In particular, SIGI-CRF analyzes non-annotated genomic sequences.
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-7-142
SIGI_CRF-AUTO
SIGI_CRF-AUTO is an alternative front-end to the SIGI-CRF processing core. First, it allows to batch process a large number of genome sequences and/or to run a variety of parameter combinations. Second, it can collect all individual prediction results generated by varying parameter combinations and combine them into a single graphical representation. Once rendered, images can be saved very flexible with a broad variety of format options.
- package colombo¶
- Versions:
4.0-1,4.0-0,3.8-1,3.8-0,v4.0-1,v4.0-0,v3.8-0- Depends:
on openjdk
- 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 colombo
to add into an existing workspace instead, run:
pixi add colombo
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 colombo
Alternatively, to install into a new environment, run:
conda create -n envname colombo
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/colombo:<tag>
(see colombo/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.
Notes¶
Wrapper scripts are provided to handle Colombo needing to be run with the working directory in its own folder
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/colombo/README.html)
