:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'pairtools' .. highlight: bash pairtools ========= .. conda:recipe:: pairtools :replaces_section_title: :noindex: CLI tools to process mapped Hi\-C data :homepage: https://github.com/open2c/pairtools :documentation: http://pairtools.readthedocs.io/ :license: MIT / MIT :recipe: /`pairtools `_/`meta.yaml `_ .. conda:package:: pairtools |downloads_pairtools| |docker_pairtools| :versions: .. raw:: html
1.0.3-01.0.2-11.0.2-01.0.1-00.3.0-60.3.0-50.3.0-40.3.0-30.3.0-2 ``1.0.3-0``,  ``1.0.2-1``,  ``1.0.2-0``,  ``1.0.1-0``,  ``0.3.0-6``,  ``0.3.0-5``,  ``0.3.0-4``,  ``0.3.0-3``,  ``0.3.0-2``,  ``0.3.0-1``,  ``0.3.0-0``,  ``0.2.2-0``,  ``0.2.1-0``,  ``0.2.0-0``,  ``0.1.1-0`` .. raw:: html
:depends bioframe: ``>=0.3.3`` :depends click: :depends coreutils: :depends htslib: :depends libgcc-ng: ``>=12`` :depends libstdcxx-ng: ``>=12`` :depends lz4-c: :depends numpy: ``>=1.21.6,<2.0a0`` :depends pandas: :depends pbgzip: :depends pysam: ``>=0.19`` :depends pysam: ``>=0.22.0,<0.23.0a0`` :depends python: ``>=3.10,<3.11.0a0`` :depends python_abi: ``3.10.* *_cp310`` :depends pyyaml: :depends samtools: :depends scipy: ``>=1.7`` :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 pairtools and update with:: mamba update pairtools To create a new environment, run:: mamba create --name myenvname pairtools 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/pairtools: (see `pairtools/tags`_ for valid values for ````) .. |downloads_pairtools| image:: https://img.shields.io/conda/dn/bioconda/pairtools.svg?style=flat :target: https://anaconda.org/bioconda/pairtools :alt: (downloads) .. |docker_pairtools| image:: https://quay.io/repository/biocontainers/pairtools/status :target: https://quay.io/repository/biocontainers/pairtools .. _`pairtools/tags`: https://quay.io/repository/biocontainers/pairtools?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/pairtools/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/pairtools/README.html