:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'micall-lite' .. highlight: bash micall-lite =========== .. conda:recipe:: micall-lite :replaces_section_title: :noindex: A bioinformatic pipeline for mapping of FASTQ data to a set of reference sequences to generate consensus sequences\, variant calls and coverage maps. :homepage: https://github.com/PoonLab/MiCall-Lite :license: GNU Affero General Public License v3.0 :recipe: /`micall-lite `_/`meta.yaml `_ .. conda:package:: micall-lite |downloads_micall-lite| |docker_micall-lite| :versions: ``0.1rc5-4``,  ``0.1rc5-3``,  ``0.1rc5-2``,  ``0.1rc5-1``,  ``0.1rc5-0``,  ``0.1rc4-0``,  ``0.1rc3-0``,  ``0.1rc2-0``,  ``0.1rc-0`` :depends bowtie2: :depends libgcc-ng: ``>=12`` :depends python: ``>=3.10,<3.11.0a0`` :depends python-levenshtein: :depends python_abi: ``3.10.* *_cp310`` :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 micall-lite and update with:: mamba update micall-lite To create a new environment, run:: mamba create --name myenvname micall-lite 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/micall-lite: (see `micall-lite/tags`_ for valid values for ````) .. |downloads_micall-lite| image:: https://img.shields.io/conda/dn/bioconda/micall-lite.svg?style=flat :target: https://anaconda.org/bioconda/micall-lite :alt: (downloads) .. |docker_micall-lite| image:: https://quay.io/repository/biocontainers/micall-lite/status :target: https://quay.io/repository/biocontainers/micall-lite .. _`micall-lite/tags`: https://quay.io/repository/biocontainers/micall-lite?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/micall-lite/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/micall-lite/README.html