:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'trycycler' .. highlight: bash trycycler ========= .. conda:recipe:: trycycler :replaces_section_title: :noindex: Trycycler is a tool for generating consensus long\-read assemblies for bacterial genomes :homepage: https://github.com/rrwick/Trycycler :license: GPLv3 :recipe: /`trycycler `_/`meta.yaml `_ .. conda:package:: trycycler |downloads_trycycler| |docker_trycycler| :versions: ``0.5.4-0``,  ``0.5.3-0``,  ``0.5.1-0``,  ``0.5.0-0``,  ``0.4.2-0``,  ``0.4.1-0``,  ``0.3.1-0`` :depends mash: :depends miniasm: :depends minimap2: :depends muscle: ``<4`` :depends numpy: :depends pillow: :depends python: ``>=3.6`` :depends python-edlib: :depends r-ape: :depends r-base: :depends r-phangorn: :depends scipy: :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 trycycler and update with:: mamba update trycycler To create a new environment, run:: mamba create --name myenvname trycycler 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/trycycler: (see `trycycler/tags`_ for valid values for ````) .. |downloads_trycycler| image:: https://img.shields.io/conda/dn/bioconda/trycycler.svg?style=flat :target: https://anaconda.org/bioconda/trycycler :alt: (downloads) .. |docker_trycycler| image:: https://quay.io/repository/biocontainers/trycycler/status :target: https://quay.io/repository/biocontainers/trycycler .. _`trycycler/tags`: https://quay.io/repository/biocontainers/trycycler?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/trycycler/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/trycycler/README.html