:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'piret' .. highlight: bash piret ===== .. conda:recipe:: piret :replaces_section_title: :noindex: A tool for conducting RNA seq analysis. :homepage: https://github.com/mshakya/PyPiReT :license: GPLV2 :recipe: /`piret `_/`meta.yaml `_ :links: biotools: :biotools:`piret` .. conda:package:: piret |downloads_piret| |docker_piret| :versions: ``0.3.4-1``,  ``0.3.4-0`` :depends argparse: :depends bamtools: ``>=2.4.0`` :depends bioconductor-deseq2: ``>=1.20.0`` :depends bioconductor-edger: ``>=3.22.5`` :depends biopython: ``>=1.7.0`` :depends hisat2: ``>=2.0.5`` :depends luigi: ``>=2.7.9`` :depends pandas: ``>=0.23.4`` :depends plumbum: ``>=1.6.0`` :depends python: :depends r: :depends samtools: ``>=1.3.1`` :depends stringtie: ``>=1.3.3`` :depends subread: ``>=1.5.0`` :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 piret and update with:: mamba update piret To create a new environment, run:: mamba create --name myenvname piret 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/piret: (see `piret/tags`_ for valid values for ````) .. |downloads_piret| image:: https://img.shields.io/conda/dn/bioconda/piret.svg?style=flat :target: https://anaconda.org/bioconda/piret :alt: (downloads) .. |docker_piret| image:: https://quay.io/repository/biocontainers/piret/status :target: https://quay.io/repository/biocontainers/piret .. _`piret/tags`: https://quay.io/repository/biocontainers/piret?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/piret/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/piret/README.html