:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'effectivet3' .. highlight: bash effectivet3 =========== .. conda:recipe:: effectivet3 :replaces_section_title: :noindex: Command line NoD \(clinod\)\, for predicting nucleolar localization sequences. :homepage: http://www.compbio.dundee.ac.uk/nod :license: Apache License, Version 2.0 + others used internally :recipe: /`effectivet3 `_/`meta.yaml `_ :links: biotools: :biotools:`effectivet3` .. conda:package:: effectivet3 |downloads_effectivet3| |docker_effectivet3| :versions: ``1.0.1-0`` :depends openjdk: ``>=6`` :depends python: ``2.7*`` :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 effectivet3 and update with:: mamba update effectivet3 To create a new environment, run:: mamba create --name myenvname effectivet3 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/effectivet3: (see `effectivet3/tags`_ for valid values for ````) .. |downloads_effectivet3| image:: https://img.shields.io/conda/dn/bioconda/effectivet3.svg?style=flat :target: https://anaconda.org/bioconda/effectivet3 :alt: (downloads) .. |docker_effectivet3| image:: https://quay.io/repository/biocontainers/effectivet3/status :target: https://quay.io/repository/biocontainers/effectivet3 .. _`effectivet3/tags`: https://quay.io/repository/biocontainers/effectivet3?tab=tags .. raw:: html Notes ----- EffectiveT3 is Java program which is packaged with a custom wrapper shell script. This shell wrapper is called \"effectivet3\" and is on \$PATH by default. By default \"\-Xms512m \-Xmx1g\" 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. For example run it with \"effectivet3 \-Xms512m \-Xmx1g ...\" 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/effectivet3/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/effectivet3/README.html