:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'samblaster' .. highlight: bash samblaster ========== .. conda:recipe:: samblaster :replaces_section_title: :noindex: Mark duplicates in and extract discordant and split reads from SAM files. :homepage: https://github.com/GregoryFaust/samblaster :license: MIT :recipe: /`samblaster `_/`meta.yaml `_ .. conda:package:: samblaster |downloads_samblaster| |docker_samblaster| :versions: .. raw:: html
0.1.26-40.1.26-30.1.26-20.1.26-10.1.26-00.1.25-00.1.24-30.1.24-20.1.24-1 ``0.1.26-4``,  ``0.1.26-3``,  ``0.1.26-2``,  ``0.1.26-1``,  ``0.1.26-0``,  ``0.1.25-0``,  ``0.1.24-3``,  ``0.1.24-2``,  ``0.1.24-1``,  ``0.1.24-0``,  ``0.1.23-0``,  ``0.1.22-0``,  ``0.1.20-4``,  ``0.1.20-3``,  ``0.1.20-2``,  ``0.1.20-1``,  ``0.1.20-0`` .. raw:: html
:depends libgcc-ng: ``>=12`` :depends libstdcxx-ng: ``>=12`` :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 samblaster and update with:: mamba update samblaster To create a new environment, run:: mamba create --name myenvname samblaster 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/samblaster: (see `samblaster/tags`_ for valid values for ````) .. |downloads_samblaster| image:: https://img.shields.io/conda/dn/bioconda/samblaster.svg?style=flat :target: https://anaconda.org/bioconda/samblaster :alt: (downloads) .. |docker_samblaster| image:: https://quay.io/repository/biocontainers/samblaster/status :target: https://quay.io/repository/biocontainers/samblaster .. _`samblaster/tags`: https://quay.io/repository/biocontainers/samblaster?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/samblaster/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/samblaster/README.html