:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'shovill-se' .. highlight: bash shovill-se ========== .. conda:recipe:: shovill-se :replaces_section_title: :noindex: An fork of Shovill \(microbial assembly pipeline for Illumina paired\-end reads\) that supports single\-end reads. :homepage: https://github.com/rpetit3/shovill :license: GPL2 :recipe: /`shovill-se `_/`meta.yaml `_ .. conda:package:: shovill-se |downloads_shovill-se| |docker_shovill-se| :versions: ``1.1.0se-2``,  ``1.1.0se-1``,  ``1.1.0se-0`` :depends bwa: ``>=0.7.17`` :depends flash: ``>=1.2`` :depends kmc: ``>=3.1`` :depends lighter: ``>=1.1`` :depends megahit: ``>=1.2.7`` :depends perl: :depends perl-file-spec: :depends perl-findbin: :depends pigz: :depends pilon: ``>=1.22`` :depends samclip: ``>=0.4`` :depends samtools: ``>=1.10`` :depends seqtk: ``>=1.3`` :depends skesa: ``>=2.2`` :depends spades: ``>=3.14`` :depends trimmomatic: ``>=0.36`` :depends velvet: ``>=1.2.10`` :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 shovill-se and update with:: mamba update shovill-se To create a new environment, run:: mamba create --name myenvname shovill-se 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/shovill-se: (see `shovill-se/tags`_ for valid values for ````) .. |downloads_shovill-se| image:: https://img.shields.io/conda/dn/bioconda/shovill-se.svg?style=flat :target: https://anaconda.org/bioconda/shovill-se :alt: (downloads) .. |docker_shovill-se| image:: https://quay.io/repository/biocontainers/shovill-se/status :target: https://quay.io/repository/biocontainers/shovill-se .. _`shovill-se/tags`: https://quay.io/repository/biocontainers/shovill-se?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/shovill-se/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/shovill-se/README.html