:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'novobreak' .. highlight: bash novobreak ========= .. conda:recipe:: novobreak :replaces_section_title: :noindex: local assembly for breakpoint detection in cancer genomes :homepage: https://github.com/czc/nb_distribution :license: MIT :recipe: /`novobreak `_/`meta.yaml `_ .. conda:package:: novobreak |downloads_novobreak| |docker_novobreak| :versions: .. raw:: html
1.1.3rc-91.1.3rc-81.1.3rc-71.1.3rc-61.1.3rc-51.1.3rc-41.1.3rc-31.1.3rc-21.1.3rc-1 ``1.1.3rc-9``,  ``1.1.3rc-8``,  ``1.1.3rc-7``,  ``1.1.3rc-6``,  ``1.1.3rc-5``,  ``1.1.3rc-4``,  ``1.1.3rc-3``,  ``1.1.3rc-2``,  ``1.1.3rc-1``,  ``1.1.3rc-0`` .. raw:: html
:depends bwa: ``>=0.7.10`` :depends libgcc-ng: ``>=12`` :depends libzlib: ``>=1.2.13,<1.3.0a0`` :depends perl: :depends samtools: ``1.*`` :depends ssake: :depends zlib: :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 novobreak and update with:: mamba update novobreak To create a new environment, run:: mamba create --name myenvname novobreak 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/novobreak: (see `novobreak/tags`_ for valid values for ````) .. |downloads_novobreak| image:: https://img.shields.io/conda/dn/bioconda/novobreak.svg?style=flat :target: https://anaconda.org/bioconda/novobreak :alt: (downloads) .. |docker_novobreak| image:: https://quay.io/repository/biocontainers/novobreak/status :target: https://quay.io/repository/biocontainers/novobreak .. _`novobreak/tags`: https://quay.io/repository/biocontainers/novobreak?tab=tags .. raw:: html Notes ----- This package makes novobreak available via a wrapper in PATH\, called \`run\_novobreak\`\, which takes all arguments of the run\_novoBreak.sh script except the first\, which is automatically inferred. 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/novobreak/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/novobreak/README.html