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

1.7.1-0,  1.6.4-1,  1.6.4-0

Depends

• blast >=2.2.31

• mmseqs2 >=8.fac81

• openjdk >=8

• python >=3.7

Required By

• braker2

Installation

With an activated Bioconda channel (see 2. 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 "-Xms1g -Xmx2g" 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.

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