:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'nullarbor' .. highlight: bash nullarbor ========= .. conda:recipe:: nullarbor :replaces_section_title: :noindex: Reads to report pipeline for bacterial isolate NGS data :homepage: https://github.com/tseemann/nullarbor :license: GPL2 :recipe: /`nullarbor `_/`meta.yaml `_ .. conda:package:: nullarbor |downloads_nullarbor| |docker_nullarbor| :versions: ``2.0.20191013-3``,  ``2.0.20191013-2``,  ``2.0.20191013-1``,  ``2.0.20191013-0``,  ``2.0.20191007-0``,  ``2.0.20191003-0``,  ``2.0.20181010-5``,  ``2.0.20181010-4``,  ``2.0.20181010-2`` :depends abricate: ``>=1.0.1`` :depends any2fasta: ``>=0.4.2`` :depends centrifuge: ``>=1.0`` :depends fasttree: ``>=2.1.10`` :depends iqtree: ``>=2.2.0`` :depends kraken: ``>=1.1`` :depends kraken2: ``>=2.1.2`` :depends make: ``>=4.2`` :depends mash: ``>=2.3`` :depends megahit: ``>=1.1.3`` :depends mlst: ``>=2.22.0`` :depends newick_utils: ``>=1.6`` :depends perl: ``5.26.2.*`` :depends perl-bioperl: ``1.7.2.*`` :depends perl-file-spec: :depends perl-file-which: :depends perl-findbin: :depends perl-json: :depends perl-list-moreutils: ``>=0.428`` :depends perl-path-tiny: :depends perl-svg: :depends perl-text-csv: :depends perl-time-piece: :depends perl-yaml-tiny: :depends pigz: :depends prokka: ``>=1.14.6`` :depends quicktree: ``>=2.5`` :depends roary: ``>=3.13`` :depends samtools: ``>=1.9`` :depends seqtk: ``>=1.3`` :depends shovill: ``>=1.1.0`` :depends skesa: ``>=2.4`` :depends snippy: ``>=4.4.3`` :depends snp-dists: ``>=0.8.2`` :depends snpeff: ``5.0.*`` :depends spades: ``>=3.15`` :depends trimmomatic: ``>=0.39`` :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 nullarbor and update with:: mamba update nullarbor To create a new environment, run:: mamba create --name myenvname nullarbor 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/nullarbor: (see `nullarbor/tags`_ for valid values for ````) .. |downloads_nullarbor| image:: https://img.shields.io/conda/dn/bioconda/nullarbor.svg?style=flat :target: https://anaconda.org/bioconda/nullarbor :alt: (downloads) .. |docker_nullarbor| image:: https://quay.io/repository/biocontainers/nullarbor/status :target: https://quay.io/repository/biocontainers/nullarbor .. _`nullarbor/tags`: https://quay.io/repository/biocontainers/nullarbor?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/nullarbor/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/nullarbor/README.html