:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'srnapipe' .. highlight: bash srnapipe ======== .. conda:recipe:: srnapipe :replaces_section_title: :noindex: Pipeline for bioinformatic in\-depth exploration of small RNA\-seq data :homepage: https://github.com/GReD-Clermont/sRNAPipe-cli :license: Academic Free License v3.0 :recipe: /`srnapipe `_/`meta.yaml `_ .. conda:package:: srnapipe |downloads_srnapipe| |docker_srnapipe| :versions: ``1.2-0``,  ``1.1.1-3``,  ``1.1.1-2``,  ``1.1.1-1``,  ``1.1.1-0``,  ``1.1-3``,  ``1.1-0`` :depends bedtools: ``>=2.24.0`` :depends bioconductor-sushi: :depends bwa: ``>=0.7.12`` :depends fonts-conda-ecosystem: :depends perl: ``>=5.32.1,<6.0a0 *_perl5`` :depends perl-file-copy-recursive: :depends perl-getopt-long: :depends perl-math-cdf: :depends perl-parallel-forkmanager: :depends perl-statistics-r: :depends perl-string-random: :depends r-base: ``>=4.1,<4.2.0a0`` :depends r-ggplot2: :depends r-plotrix: :depends r-rcolorbrewer: :depends samtools: ``>=1.5`` :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 srnapipe and update with:: mamba update srnapipe To create a new environment, run:: mamba create --name myenvname srnapipe 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/srnapipe: (see `srnapipe/tags`_ for valid values for ````) .. |downloads_srnapipe| image:: https://img.shields.io/conda/dn/bioconda/srnapipe.svg?style=flat :target: https://anaconda.org/bioconda/srnapipe :alt: (downloads) .. |docker_srnapipe| image:: https://quay.io/repository/biocontainers/srnapipe/status :target: https://quay.io/repository/biocontainers/srnapipe .. _`srnapipe/tags`: https://quay.io/repository/biocontainers/srnapipe?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/srnapipe/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/srnapipe/README.html