:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'ribotricer' .. highlight: bash ribotricer ========== .. conda:recipe:: ribotricer :replaces_section_title: :noindex: Python package to detect translating ORF from Ribo\-seq data :homepage: https://github.com/smithlabcode/ribotricer :license: GPL3 / GNU General Public v3 (GPLv3) :recipe: /`ribotricer `_/`meta.yaml `_ Ribotricer is a method for detecting actively\-translating ORFs by directly leveraging the three\-nucleotide periodicity of Ribo\-seq data. It accurately identifies both short and long active ORFs. .. conda:package:: ribotricer |downloads_ribotricer| |docker_ribotricer| :versions: ``1.3.3-0``,  ``1.3.2-0``,  ``1.3.1-0``,  ``1.3.0-0``,  ``1.2.0-0``,  ``1.1.1-0``,  ``1.1.0-0``,  ``1.0.3-0``,  ``1.0.2-0`` :depends click: ``>=6.0`` :depends click-help-colors: ``>=0.3`` :depends matplotlib-base: ``>=2.1.0`` :depends numpy: ``>=1.11.0`` :depends pandas: ``>=0.20.3`` :depends pyfaidx: ``>=0.5.0`` :depends pysam: ``>=0.11.2.2`` :depends python: ``>3`` :depends quicksect: ``>=0.2.0`` :depends scipy: ``>=0.19.1`` :depends tqdm: ``>=4.23.4`` :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 ribotricer and update with:: mamba update ribotricer To create a new environment, run:: mamba create --name myenvname ribotricer 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/ribotricer: (see `ribotricer/tags`_ for valid values for ````) .. |downloads_ribotricer| image:: https://img.shields.io/conda/dn/bioconda/ribotricer.svg?style=flat :target: https://anaconda.org/bioconda/ribotricer :alt: (downloads) .. |docker_ribotricer| image:: https://quay.io/repository/biocontainers/ribotricer/status :target: https://quay.io/repository/biocontainers/ribotricer .. _`ribotricer/tags`: https://quay.io/repository/biocontainers/ribotricer?tab=tags .. raw:: html 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/ribotricer/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/ribotricer/README.html