:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'extract-sv-reads' .. highlight: bash extract-sv-reads ================ .. conda:recipe:: extract-sv-reads :replaces_section_title: :noindex: Tool for extracting splitter or discordant reads from a BAM or CRAM file. :homepage: https://github.com/hall-lab/extract_sv_reads :license: MIT :recipe: /`extract-sv-reads `_/`meta.yaml `_ .. conda:package:: extract-sv-reads |downloads_extract-sv-reads| |docker_extract-sv-reads| :versions: ``1.3.0-4``,  ``1.3.0-3``,  ``1.3.0-2``,  ``1.3.0-1``,  ``1.3.0-0``,  ``1.2.1-1``,  ``1.2.1-0``,  ``1.1.2-0``,  ``1.1.0-0`` :depends boost-cpp: ``>=1.78.0,<1.78.1.0a0`` :depends htslib: ``>=1.9,<1.10.0a0`` :depends libgcc-ng: ``>=12`` :depends libstdcxx-ng: ``>=12`` :depends perl: ``>=5.32.1,<5.33.0a0 *_perl5`` :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 extract-sv-reads and update with:: mamba update extract-sv-reads To create a new environment, run:: mamba create --name myenvname extract-sv-reads 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/extract-sv-reads: (see `extract-sv-reads/tags`_ for valid values for ````) .. |downloads_extract-sv-reads| image:: https://img.shields.io/conda/dn/bioconda/extract-sv-reads.svg?style=flat :target: https://anaconda.org/bioconda/extract-sv-reads :alt: (downloads) .. |docker_extract-sv-reads| image:: https://quay.io/repository/biocontainers/extract-sv-reads/status :target: https://quay.io/repository/biocontainers/extract-sv-reads .. _`extract-sv-reads/tags`: https://quay.io/repository/biocontainers/extract-sv-reads?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/extract-sv-reads/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/extract-sv-reads/README.html