:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'samtools' .. highlight: bash samtools ======== .. conda:recipe:: samtools :replaces_section_title: :noindex: Tools for dealing with SAM\, BAM and CRAM files :homepage: https://github.com/samtools/samtools :license: MIT :recipe: /`samtools `_/`meta.yaml `_ :links: biotools: :biotools:`samtools`, usegalaxy-eu: :usegalaxy-eu:`samtools_flagstat` .. conda:package:: samtools |downloads_samtools| |docker_samtools| :versions: .. raw:: html
1.19.2-11.19.2-01.19.1-01.19-01.18-11.18-01.17-21.17-11.17-0 ``1.19.2-1``,  ``1.19.2-0``,  ``1.19.1-0``,  ``1.19-0``,  ``1.18-1``,  ``1.18-0``,  ``1.17-2``,  ``1.17-1``,  ``1.17-0``,  ``1.16.1-2``,  ``1.16.1-1``,  ``1.16.1-0``,  ``1.15.1-1``,  ``1.15.1-0``,  ``1.15-1``,  ``1.15-0``,  ``1.14-0``,  ``1.13-0``,  ``1.12-1``,  ``1.12-0``,  ``1.11-0``,  ``1.10-3``,  ``1.10-2``,  ``1.10-1``,  ``1.10-0``,  ``1.9-12``,  ``1.9-11``,  ``1.9-10``,  ``1.9-9``,  ``1.9-8``,  ``1.9-7``,  ``1.9-6``,  ``1.9-5``,  ``1.9-4``,  ``1.9-3``,  ``1.9-2``,  ``1.9-1``,  ``1.9-0``,  ``1.8-5``,  ``1.8-4``,  ``1.8-3``,  ``1.8-2``,  ``1.7-2``,  ``1.7-1``,  ``1.7-0``,  ``1.6-10``,  ``1.6-9``,  ``1.6-8``,  ``1.6-7``,  ``1.6-6``,  ``1.6-5``,  ``1.6-4``,  ``1.6-3``,  ``1.6-2``,  ``1.6-1``,  ``1.6-0``,  ``1.5-2``,  ``1.5-1``,  ``1.5-0``,  ``1.4.1-0``,  ``1.4-0``,  ``1.3.1-11``,  ``1.3.1-10``,  ``1.3.1-9``,  ``1.3.1-8``,  ``1.3.1-7``,  ``1.3.1-6``,  ``1.3.1-5``,  ``1.3.1-4``,  ``1.3.1-3``,  ``1.3.1-2``,  ``1.3.1-1``,  ``1.3.1-0``,  ``1.3-8``,  ``1.3-7``,  ``1.3-6``,  ``1.3-5``,  ``1.3-4``,  ``1.3-3``,  ``1.3-2``,  ``1.3-1``,  ``1.3-0``,  ``1.2-2``,  ``1.2-1``,  ``1.2-0``,  ``1.2.rglab-1``,  ``1.2.rglab-0``,  ``1.1-8``,  ``1.1-7``,  ``1.1-6``,  ``1.1-5``,  ``1.1-4``,  ``1.1-3``,  ``1.1-1``,  ``1.1-0``,  ``1.0-2``,  ``1.0-1``,  ``1.0-0``,  ``0.1.19-11``,  ``0.1.19-10``,  ``0.1.19-9``,  ``0.1.19-8``,  ``0.1.19-7``,  ``0.1.19-6``,  ``0.1.19-5``,  ``0.1.19-4``,  ``0.1.19-3``,  ``0.1.19-2``,  ``0.1.19-1``,  ``0.1.19-0``,  ``0.1.18-13``,  ``0.1.18-12``,  ``0.1.18-11``,  ``0.1.18-10``,  ``0.1.18-0``,  ``0.1.17-0``,  ``0.1.16-0``,  ``0.1.15-1``,  ``0.1.15-0``,  ``0.1.14-2``,  ``0.1.14-1``,  ``0.1.14-0``,  ``0.1.13-2``,  ``0.1.13-1``,  ``0.1.13-0``,  ``0.1.12-3``,  ``0.1.12-2``,  ``0.1.12-1``,  ``0.1.12-0`` .. raw:: html
:depends htslib: ``>=1.19.1,<1.20.0a0`` :depends libgcc-ng: ``>=12`` :depends libzlib: ``>=1.2.13,<1.3.0a0`` :depends ncurses: ``>=6.4,<7.0a0`` :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 samtools and update with:: mamba update samtools To create a new environment, run:: mamba create --name myenvname samtools 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/samtools: (see `samtools/tags`_ for valid values for ````) .. |downloads_samtools| image:: https://img.shields.io/conda/dn/bioconda/samtools.svg?style=flat :target: https://anaconda.org/bioconda/samtools :alt: (downloads) .. |docker_samtools| image:: https://quay.io/repository/biocontainers/samtools/status :target: https://quay.io/repository/biocontainers/samtools .. _`samtools/tags`: https://quay.io/repository/biocontainers/samtools?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/samtools/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/samtools/README.html