:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'isoquant' .. highlight: bash isoquant ======== .. conda:recipe:: isoquant :replaces_section_title: :noindex: IsoQuant is a tool for reference\-based analysis of long RNA reads\, such as gene\/transcript quantification and discovery. :homepage: https://github.com/ablab/IsoQuant :license: GPL2 :recipe: /`isoquant `_/`meta.yaml `_ .. conda:package:: isoquant |downloads_isoquant| |docker_isoquant| :versions: .. raw:: html
3.3.1-03.3.0-03.2.0-03.1.2-13.1.2-03.1.1-03.1.0-03.0.3-03.0.1-0 ``3.3.1-0``,  ``3.3.0-0``,  ``3.2.0-0``,  ``3.1.2-1``,  ``3.1.2-0``,  ``3.1.1-0``,  ``3.1.0-0``,  ``3.0.3-0``,  ``3.0.1-0``,  ``3.0.0-0``,  ``2.3.0-0``,  ``2.2.2-0``,  ``2.2.1-0``,  ``2.2.0-1``,  ``2.2.0-0``,  ``2.1.1-0``,  ``2.1.0-0``,  ``2.0.0-0``,  ``1.3.0-0``,  ``1.2.2-0``,  ``1.2.1-1``,  ``1.2.1-0``,  ``1.2.0-1``,  ``1.2.0-0``,  ``1.1.0-1``,  ``1.1.0-0``,  ``1.0.0-0`` .. raw:: html
:depends argcomplete: ``>=1.11.1`` :depends argh: ``>=0.26.2`` :depends biopython: ``>=1.76`` :depends gffutils: ``>=0.10.1`` :depends minimap2: ``>=2.18`` :depends pandas: ``>=1.0`` :depends pybedtools: ``>=0.8.1`` :depends pyfaidx: ``>=0.5.8`` :depends pysam: ``>=0.15`` :depends python: ``>=3.7`` :depends samtools: ``>=1.14`` :depends simplejson: ``>=3.17.0`` :depends six: ``>=1.14.0`` :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 isoquant and update with:: mamba update isoquant To create a new environment, run:: mamba create --name myenvname isoquant 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/isoquant: (see `isoquant/tags`_ for valid values for ````) .. |downloads_isoquant| image:: https://img.shields.io/conda/dn/bioconda/isoquant.svg?style=flat :target: https://anaconda.org/bioconda/isoquant :alt: (downloads) .. |docker_isoquant| image:: https://quay.io/repository/biocontainers/isoquant/status :target: https://quay.io/repository/biocontainers/isoquant .. _`isoquant/tags`: https://quay.io/repository/biocontainers/isoquant?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/isoquant/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/isoquant/README.html