:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'pysam' .. highlight: bash pysam ===== .. conda:recipe:: pysam :replaces_section_title: :noindex: Pysam is a Python module for reading and manipulating SAM\/BAM\/VCF\/BCF files. It\'s a lightweight wrapper of the htslib C\-API\, the same one that powers samtools\, bcftools\, and tabix. :homepage: https://github.com/pysam-developers/pysam :license: MIT :recipe: /`pysam `_/`meta.yaml `_ :links: biotools: :biotools:`pysam`, doi: :doi:`10.1093/bioinformatics/btp352` .. conda:package:: pysam |downloads_pysam| |docker_pysam| :versions: .. raw:: html
0.22.0-10.22.0-00.21.0-10.21.0-00.20.0-00.19.1-10.19.1-00.19.0-00.18.0-2 ``0.22.0-1``,  ``0.22.0-0``,  ``0.21.0-1``,  ``0.21.0-0``,  ``0.20.0-0``,  ``0.19.1-1``,  ``0.19.1-0``,  ``0.19.0-0``,  ``0.18.0-2``,  ``0.18.0-1``,  ``0.18.0-0``,  ``0.17.0-1``,  ``0.17.0-0``,  ``0.16.0.1-3``,  ``0.16.0.1-2``,  ``0.16.0.1-1``,  ``0.16.0.1-0``,  ``0.16.0-1``,  ``0.16.0-0``,  ``0.15.4-1``,  ``0.15.4-0``,  ``0.15.3-3``,  ``0.15.3-1``,  ``0.15.3-0``,  ``0.15.2-11``,  ``0.15.2-10``,  ``0.15.2-9``,  ``0.15.2-8``,  ``0.15.2-7``,  ``0.15.2-6``,  ``0.15.2-5``,  ``0.15.2-4``,  ``0.15.2-3``,  ``0.15.2-2``,  ``0.15.2-1``,  ``0.15.2-0``,  ``0.15.1-0``,  ``0.15.0.1-1``,  ``0.15.0.1-0``,  ``0.15.0-0``,  ``0.14.1-1``,  ``0.14.1-0``,  ``0.14.0-2``,  ``0.14.0-1``,  ``0.14.0-0``,  ``0.13.0-0``,  ``0.12.0.1-2``,  ``0.12.0.1-1``,  ``0.12.0.1-0``,  ``0.11.2.2-2``,  ``0.11.2.2-1``,  ``0.11.2.2-0``,  ``0.11.2.1-0``,  ``0.11.1-0``,  ``0.11.0-0``,  ``0.10.0-13``,  ``0.10.0-12``,  ``0.10.0-11``,  ``0.10.0-10``,  ``0.10.0-9``,  ``0.10.0-8``,  ``0.10.0-7``,  ``0.10.0-6``,  ``0.10.0-5``,  ``0.10.0-4``,  ``0.10.0-3``,  ``0.10.0-1``,  ``0.9.1.4-1``,  ``0.9.1.4-0``,  ``0.9.1-12``,  ``0.9.1-11``,  ``0.9.1-10``,  ``0.9.1-9``,  ``0.9.1-8``,  ``0.9.1-7``,  ``0.9.1-6``,  ``0.9.1-5``,  ``0.9.1-4``,  ``0.9.1-3``,  ``0.9.1-2``,  ``0.9.1-1``,  ``0.9.1-0``,  ``0.9.0-2``,  ``0.9.0-1``,  ``0.9.0-0``,  ``0.8.4-0``,  ``0.8.4pre0-0``,  ``0.8.3-9``,  ``0.8.3-8``,  ``0.8.3-7``,  ``0.8.3-6``,  ``0.8.3-5``,  ``0.8.3-4``,  ``0.8.3-3``,  ``0.8.3-2``,  ``0.8.3-1``,  ``0.8.3-0``,  ``0.7.7-6``,  ``0.7.7-5``,  ``0.7.7-4``,  ``0.7.7-3``,  ``0.7.7-2``,  ``0.7.7-1``,  ``0.7.7-0`` .. raw:: html
:depends bzip2: ``>=1.0.8,<2.0a0`` :depends libcurl: ``>=8.5.0,<9.0a0`` :depends libdeflate: ``>=1.18,<1.19.0a0`` :depends libgcc-ng: ``>=12`` :depends libzlib: ``>=1.2.13,<1.3.0a0`` :depends openssl: ``>=3.2.1,<4.0a0`` :depends python: ``>=3.10,<3.11.0a0`` :depends python_abi: ``3.10.* *_cp310`` :depends xz: ``>=5.2.6,<6.0a0`` :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 pysam and update with:: mamba update pysam To create a new environment, run:: mamba create --name myenvname pysam 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/pysam: (see `pysam/tags`_ for valid values for ````) .. |downloads_pysam| image:: https://img.shields.io/conda/dn/bioconda/pysam.svg?style=flat :target: https://anaconda.org/bioconda/pysam :alt: (downloads) .. |docker_pysam| image:: https://quay.io/repository/biocontainers/pysam/status :target: https://quay.io/repository/biocontainers/pysam .. _`pysam/tags`: https://quay.io/repository/biocontainers/pysam?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/pysam/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/pysam/README.html