- 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:
- License:
GPL3
- Recipe:
- 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:
on blast
>=2.12.0on mmseqs2
>=14.7e284on openjdk
>=8,<12on python
>=3.7
- 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 gemoma
to add into an existing workspace instead, run:
pixi add gemoma
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 gemoma
Alternatively, to install into a new environment, run:
conda create -n envname gemoma
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/gemoma:<tag>
(see gemoma/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¶
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:
[](http://bioconda.github.io/recipes/gemoma/README.html)
