:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'pipmir' .. highlight: bash pipmir ====== .. conda:recipe:: pipmir :replaces_section_title: :noindex: We developed the PIPmiR algorithm to identify novel plant miRNA genes from a combination of deep sequencing data and genomic features. :homepage: https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/ :license: PIPmiR is provided for academic use only, if you wish to use it in another setting please contact Uwe Ohler. :recipe: /`pipmir `_/`meta.yaml `_ :links: biotools: :biotools:`pipmir`, doi: :doi:`10.1101/gr.123547.111` .. conda:package:: pipmir |downloads_pipmir| |docker_pipmir| :versions: ``1.1-5``,  ``1.1-4``,  ``1.1-3``,  ``1.1-2``,  ``1.1-1`` :depends openjdk: :depends samtools: :depends viennarna: ``1.8.5.*`` :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 pipmir and update with:: mamba update pipmir To create a new environment, run:: mamba create --name myenvname pipmir 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/pipmir: (see `pipmir/tags`_ for valid values for ````) .. |downloads_pipmir| image:: https://img.shields.io/conda/dn/bioconda/pipmir.svg?style=flat :target: https://anaconda.org/bioconda/pipmir :alt: (downloads) .. |docker_pipmir| image:: https://quay.io/repository/biocontainers/pipmir/status :target: https://quay.io/repository/biocontainers/pipmir .. _`pipmir/tags`: https://quay.io/repository/biocontainers/pipmir?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/pipmir/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/pipmir/README.html