:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'cgat-apps' .. highlight: bash cgat-apps ========= .. conda:recipe:: cgat-apps :replaces_section_title: :noindex: Computational Genomics Analysis Toolkit :homepage: https://cgat-apps.readthedocs.io/en/latest/ :license: MIT :recipe: /`cgat-apps `_/`meta.yaml `_ .. conda:package:: cgat-apps |downloads_cgat-apps| |docker_cgat-apps| :versions: .. raw:: html
0.6.5-30.6.5-20.6.5-10.6.5-00.6.4-10.6.4-00.6.0-20.6.0-10.6.0-0 ``0.6.5-3``,  ``0.6.5-2``,  ``0.6.5-1``,  ``0.6.5-0``,  ``0.6.4-1``,  ``0.6.4-0``,  ``0.6.0-2``,  ``0.6.0-1``,  ``0.6.0-0``,  ``0.5.6-0``,  ``0.5.5-0``,  ``0.5.4-0``,  ``0.5.3-0`` .. raw:: html
:depends alignlib-lite: :depends bedtools: :depends biopython: :depends cgatcore: ``>=0.6.5`` :depends coreutils: :depends future: :depends grep: :depends htslib: ``>=1.16,<1.20.0a0`` :depends jinja2: :depends libcxx: ``>=14.0.4`` :depends matplotlib-base: :depends numpy: ``>=1.21.6,<2.0a0`` :depends pandas: :depends pybedtools: :depends pybigwig: :depends pysam: ``>=0.17.0`` :depends python: ``>=3.10,<3.11.0a0`` :depends python_abi: ``3.10.* *_cp310`` :depends pyyaml: :depends quicksect: :depends scikit-learn: :depends scipy: :depends six: :depends sortedcontainers: :depends ucsc-bedgraphtobigwig: :depends ucsc-bedtobigbed: :depends ucsc-wigtobigwig: :depends zlib: ``>=1.2.12,<1.3.0a0`` :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 cgat-apps and update with:: mamba update cgat-apps To create a new environment, run:: mamba create --name myenvname cgat-apps 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/cgat-apps: (see `cgat-apps/tags`_ for valid values for ````) .. |downloads_cgat-apps| image:: https://img.shields.io/conda/dn/bioconda/cgat-apps.svg?style=flat :target: https://anaconda.org/bioconda/cgat-apps :alt: (downloads) .. |docker_cgat-apps| image:: https://quay.io/repository/biocontainers/cgat-apps/status :target: https://quay.io/repository/biocontainers/cgat-apps .. _`cgat-apps/tags`: https://quay.io/repository/biocontainers/cgat-apps?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/cgat-apps/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/cgat-apps/README.html