:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'shortstack' .. highlight: bash shortstack ========== .. conda:recipe:: shortstack :replaces_section_title: :noindex: ShortStack\: Comprehensive annotation and quantification of small RNA genes :homepage: https://github.com/MikeAxtell/ShortStack :license: MIT / MIT :recipe: /`shortstack `_/`meta.yaml `_ .. conda:package:: shortstack |downloads_shortstack| |docker_shortstack| :versions: .. raw:: html
4.0.3-04.0.2-04.0.1-04.0.0-03.8.5-43.8.5-33.8.5-23.8.5-13.8.5-0 ``4.0.3-0``,  ``4.0.2-0``,  ``4.0.1-0``,  ``4.0.0-0``,  ``3.8.5-4``,  ``3.8.5-3``,  ``3.8.5-2``,  ``3.8.5-1``,  ``3.8.5-0``,  ``3.8.3-0``,  ``3.6-1``,  ``3.6-0`` .. raw:: html
:depends bedtools: :depends biopython: :depends bowtie: ``>=1.3.1`` :depends cutadapt: :depends numpy: :depends python: ``>=3.10.8`` :depends samtools: ``>=1.16`` :depends shorttracks: :depends strucvis: :depends tqdm: :depends viennarna: ``2.*`` :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 shortstack and update with:: mamba update shortstack To create a new environment, run:: mamba create --name myenvname shortstack 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/shortstack: (see `shortstack/tags`_ for valid values for ````) .. |downloads_shortstack| image:: https://img.shields.io/conda/dn/bioconda/shortstack.svg?style=flat :target: https://anaconda.org/bioconda/shortstack :alt: (downloads) .. |docker_shortstack| image:: https://quay.io/repository/biocontainers/shortstack/status :target: https://quay.io/repository/biocontainers/shortstack .. _`shortstack/tags`: https://quay.io/repository/biocontainers/shortstack?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/shortstack/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/shortstack/README.html