:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'saspector' .. highlight: bash saspector ========= .. conda:recipe:: saspector :replaces_section_title: :noindex: A tool for analysis of missing regions in \(bacterial\) draft genomes. :homepage: https://github.com/alejocrojo09/SASpector :license: MIT :recipe: /`saspector `_/`meta.yaml `_ .. conda:package:: saspector |downloads_saspector| |docker_saspector| :versions: ``0.0.5-0``,  ``0.0.3-0``,  ``0.0.1-0`` :depends biopython: :depends blast: :depends matplotlib-base: :depends numpy: :depends pandas: :depends progressbar: :depends progressivemauve: :depends prokka: :depends python: ``>3`` :depends quast: :depends samtools: :depends seaborn: :depends sourmash: :depends trf: :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 saspector and update with:: mamba update saspector To create a new environment, run:: mamba create --name myenvname saspector 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/saspector: (see `saspector/tags`_ for valid values for ````) .. |downloads_saspector| image:: https://img.shields.io/conda/dn/bioconda/saspector.svg?style=flat :target: https://anaconda.org/bioconda/saspector :alt: (downloads) .. |docker_saspector| image:: https://quay.io/repository/biocontainers/saspector/status :target: https://quay.io/repository/biocontainers/saspector .. _`saspector/tags`: https://quay.io/repository/biocontainers/saspector?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/saspector/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/saspector/README.html