recipe gemoma

Gene Model Mapper (GeMoMa) is a homology-based gene prediction program. GeMoMa uses the annotation of protein-coding genes in a reference genome to infer the annotation of protein-coding genes in a target genome. Thereby, GeMoMa utilizes amino acid sequence and intron position conservation. In addition, GeMoMa allows to incorporate RNA-seq evidence for splice site prediction.

Homepage:

http://www.jstacs.de/index.php/GeMoMa

License:

GPL3

Recipe:

/gemoma/meta.yaml

Links:

doi: 10.1093/nar/gkw092, doi: 10.1186/s12859-018-2203-5

package gemoma

Versions:

1.9-0,  1.7.1-0,  1.6.4-1,  1.6.4-0

Depends:

• blast >=2.12.0

• mmseqs2 >=14.7e284

• openjdk >=8,<12

• python >=3.7

Required By:

• braker2

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install gemoma

and update with:

conda update gemoma

or use the docker container:

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

(see gemoma/tags for valid values for <tag>)

Notes

GeMoMa is Java program that comes with a custom wrapper python script. By default "-Xms3g -Xmx6g" is set in the wrapper. If you want to overwrite it you can specify these values directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence.

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/gemoma/README.html)