:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'brass' .. highlight: bash brass ===== .. conda:recipe:: brass :replaces_section_title: :noindex: BRASS analyses one or more related BAM files of paired\-end sequencing to determine potential rearrangement breakpoints. :homepage: https://github.com/cancerit/BRASS :license: AGPL-3-0 :recipe: /`brass `_/`meta.yaml `_ .. conda:package:: brass |downloads_brass| |docker_brass| :versions: ``5.1.6-7``,  ``5.1.6-2`` :depends bedtools: :depends blat: :depends cansam: :depends exonerate: :depends libgcc: :depends perl-bio-db-hts: :depends perl-bio-featureio: :depends perl-bioperl-core: ``==1.6.924`` :depends perl-capture-tiny: :depends perl-file-sharedir: :depends perl-file-sharedir-install: :depends perl-graph-readwrite: :depends perl-grass: :depends perl-math-combinatorics: :depends perl-number-format: :depends perl-pcap: :depends perl-statistics-basic: :depends perl-text-diff: :depends velvet: :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 brass and update with:: mamba update brass To create a new environment, run:: mamba create --name myenvname brass 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/brass: (see `brass/tags`_ for valid values for ````) .. |downloads_brass| image:: https://img.shields.io/conda/dn/bioconda/brass.svg?style=flat :target: https://anaconda.org/bioconda/brass :alt: (downloads) .. |docker_brass| image:: https://quay.io/repository/biocontainers/brass/status :target: https://quay.io/repository/biocontainers/brass .. _`brass/tags`: https://quay.io/repository/biocontainers/brass?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/brass/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/brass/README.html