:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'hatchet' .. highlight: bash hatchet ======= .. conda:recipe:: hatchet :replaces_section_title: :noindex: A package to infer allele and clone\-specific copy\-number aberrations \(CNAs\). :homepage: https://github.com/raphael-group/hatchet :documentation: https://raphael-group.github.io/hatchet/ :license: BSD / BSD-3-Clause :recipe: /`hatchet `_/`meta.yaml `_ HATCHet is an algorithm to infer allele and clone\-specific copy\-number aberrations \(CNAs\)\, clone proportions\, and whole\-genome duplications \(WGD\) for several tumor clones jointly from multiple bulk\-tumor samples of the same patient or from a single bulk\-tumor sample. .. conda:package:: hatchet |downloads_hatchet| |docker_hatchet| :versions: .. raw:: html
2.0.1-01.1.1-11.1.1-01.1.0-01.0.3-01.0.2-01.0.1-01.0.0-00.4.14-0 ``2.0.1-0``,  ``1.1.1-1``,  ``1.1.1-0``,  ``1.1.0-0``,  ``1.0.3-0``,  ``1.0.2-0``,  ``1.0.1-0``,  ``1.0.0-0``,  ``0.4.14-0``,  ``0.4.12-1``,  ``0.4.12-0``,  ``0.4.11-0``,  ``0.4.10-0``,  ``0.4.9-0``,  ``0.4.7-0``,  ``0.4.6-0``,  ``0.4.5-0``,  ``0.4.4-0``,  ``0.4.3-0``,  ``0.4.2-0``,  ``0.4.1-0``,  ``0.3.3-0``,  ``0.3.2-0``,  ``0.3.1-0``,  ``0.3.0-0``,  ``0.2.11-0``,  ``0.2.10-0``,  ``0.2.9-3``,  ``0.2.9-1``,  ``0.2.9-0`` .. raw:: html
:depends bcftools: ``>=1.9`` :depends biopython: :depends hmmlearn: :depends libgcc-ng: ``>=12`` :depends libstdcxx-ng: ``>=12`` :depends matplotlib-base: :depends mosdepth: :depends pandas: :depends picard-slim: :depends psutil: :depends pyomo: :depends pysam: :depends python: ``>=3.10,<3.11.0a0`` :depends python_abi: ``3.10.* *_cp310`` :depends requests: :depends samtools: ``>=1.9`` :depends scikit-learn: :depends scipy: :depends seaborn: :depends tabix: :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 hatchet and update with:: mamba update hatchet To create a new environment, run:: mamba create --name myenvname hatchet 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/hatchet: (see `hatchet/tags`_ for valid values for ````) .. |downloads_hatchet| image:: https://img.shields.io/conda/dn/bioconda/hatchet.svg?style=flat :target: https://anaconda.org/bioconda/hatchet :alt: (downloads) .. |docker_hatchet| image:: https://quay.io/repository/biocontainers/hatchet/status :target: https://quay.io/repository/biocontainers/hatchet .. _`hatchet/tags`: https://quay.io/repository/biocontainers/hatchet?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/hatchet/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/hatchet/README.html