recipe colombo

A software framework equipped with a GUI for the prediction of genomic islands (GIs) in prokaryotes.

Homepage:

https://www.uni-goettingen.de/en/research/185810.html

License:

Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)

Recipe:

/colombo/meta.yaml

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

(downloads) docker_colombo

versions:

4.0-1,  4.0-0,  3.8-1,  3.8-0,  v4.0-1,  v4.0-0,  v3.8-0

depends openjdk:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install colombo

and update with::

   mamba update colombo

To create a new environment, run:

mamba create --name myenvname colombo

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/colombo:<tag>

(see `colombo/tags`_ for valid values for ``<tag>``)

Notes

Wrapper scripts are provided to handle Colombo needing to be run with the working directory in its own folder

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