:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'gemoma' .. highlight: bash gemoma ====== .. conda:recipe:: gemoma :replaces_section_title: :noindex: 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: :doi:`10.1093/nar/gkw092`, doi: :doi:`10.1186/s12859-018-2203-5` .. conda:package:: gemoma |downloads_gemoma| |docker_gemoma| :versions: ``1.9-0``,  ``1.7.1-0``,  ``1.6.4-1``,  ``1.6.4-0`` :depends blast: ``>=2.12.0`` :depends mmseqs2: ``>=14.7e284`` :depends openjdk: ``>=8,<12`` :depends python: ``>=3.7`` :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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 gemoma and update with:: mamba update gemoma To create a new environment, run:: mamba create --name myenvname gemoma 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/gemoma: (see `gemoma/tags`_ for valid values for ````) .. |downloads_gemoma| image:: https://img.shields.io/conda/dn/bioconda/gemoma.svg?style=flat :target: https://anaconda.org/bioconda/gemoma :alt: (downloads) .. |docker_gemoma| image:: https://quay.io/repository/biocontainers/gemoma/status :target: https://quay.io/repository/biocontainers/gemoma .. _`gemoma/tags`: https://quay.io/repository/biocontainers/gemoma?tab=tags .. raw:: html 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 ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| 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) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/gemoma/README.html