:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'spectra-cluster-cli' .. highlight: bash spectra-cluster-cli =================== .. conda:recipe:: spectra-cluster-cli :replaces_section_title: :noindex: This is a stand\-alone implementation of the new updated PRIDE Cluster algorithm. It is based on the spectra\-cluster API and uses a highly similar logic as the Hadoop implementation spectra\-cluster\-hadoop used to build the PRIDE Cluster resource. :homepage: https://github.com/spectra-cluster/spectra-cluster-cli :license: Apache / Apache-2.0 :recipe: /`spectra-cluster-cli `_/`meta.yaml `_ .. conda:package:: spectra-cluster-cli |downloads_spectra-cluster-cli| |docker_spectra-cluster-cli| :versions: ``1.1.2-1``,  ``1.1.2-0``,  ``1.0.1-1``,  ``1.0.1-0`` :depends openjdk: ``>=6`` :depends python: :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 spectra-cluster-cli and update with:: mamba update spectra-cluster-cli To create a new environment, run:: mamba create --name myenvname spectra-cluster-cli 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/spectra-cluster-cli: (see `spectra-cluster-cli/tags`_ for valid values for ````) .. |downloads_spectra-cluster-cli| image:: https://img.shields.io/conda/dn/bioconda/spectra-cluster-cli.svg?style=flat :target: https://anaconda.org/bioconda/spectra-cluster-cli :alt: (downloads) .. |docker_spectra-cluster-cli| image:: https://quay.io/repository/biocontainers/spectra-cluster-cli/status :target: https://quay.io/repository/biocontainers/spectra-cluster-cli .. _`spectra-cluster-cli/tags`: https://quay.io/repository/biocontainers/spectra-cluster-cli?tab=tags .. raw:: html Notes ----- spectra\-cluster\-cli is Java program that comes with a custom wrapper shell script. This shell wrapper is called \"opsin\" 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 \"spectra\-cluster\-cli \-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/spectra-cluster-cli/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/spectra-cluster-cli/README.html