:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'ggcaller' .. highlight: bash ggcaller ======== .. conda:recipe:: ggcaller :replaces_section_title: :noindex: A de Bruijn graph\-based gene\-caller and pangenome analysis tool :homepage: https://github.com/samhorsfield96/ggCaller :license: MIT / MIT :recipe: /`ggcaller `_/`meta.yaml `_ .. conda:package:: ggcaller |downloads_ggcaller| |docker_ggcaller| :versions: .. raw:: html
1.3.4-01.3.3-11.3.3-01.3.2-01.3.1-01.3.0-11.3.0-01.2.4-21.2.4-1 ``1.3.4-0``,  ``1.3.3-1``,  ``1.3.3-0``,  ``1.3.2-0``,  ``1.3.1-0``,  ``1.3.0-1``,  ``1.3.0-0``,  ``1.2.4-2``,  ``1.2.4-1``,  ``1.2.4-0``,  ``1.2.3-0``,  ``1.2.2-0``,  ``1.2.1-0``,  ``1.1.1-0``,  ``1.0.0-0`` .. raw:: html
:depends _openmp_mutex: ``>=4.5`` :depends bcbio-gff: :depends bifrost: :depends biopython: ``>=1.8.0`` :depends boost-cpp: ``>=1.78.0,<1.78.1.0a0`` :depends bzip2: ``>=1.0.8,<2.0a0`` :depends cd-hit: :depends diamond: ``>=2.0`` :depends gffutils: :depends hmmer: :depends intbitset: :depends joblib: :depends libgcc-ng: ``>=12`` :depends libstdcxx-ng: ``>=12`` :depends libzlib: ``>=1.2.13,<1.3.0a0`` :depends mafft: :depends matplotlib-base: :depends mkl: ``>=2022.2.1,<2023.0a0`` :depends networkx: :depends numpy: :depends pandas: :depends pthread-stubs: :depends python: ``>=3.10,<3.11.0a0`` :depends python-edlib: :depends python-wget: :depends python_abi: ``3.10.* *_cp310`` :depends pytorch: ``>=1.13.1,<1.14.0a0`` :depends rapidnj: :depends scipy: :depends seaborn: :depends snp-sites: :depends tbb: ``>=2021.9.0`` :depends tqdm: :depends uncertainties: :depends xorg-libxaw: :depends xorg-libxcomposite: :depends xorg-libxcursor: :depends xorg-libxdamage: :depends xorg-libxfixes: :depends xorg-libxi: :depends xorg-libxinerama: :depends xorg-libxpm: :depends xorg-libxrandr: :depends zlib: :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 ggcaller and update with:: mamba update ggcaller To create a new environment, run:: mamba create --name myenvname ggcaller 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/ggcaller: (see `ggcaller/tags`_ for valid values for ````) .. |downloads_ggcaller| image:: https://img.shields.io/conda/dn/bioconda/ggcaller.svg?style=flat :target: https://anaconda.org/bioconda/ggcaller :alt: (downloads) .. |docker_ggcaller| image:: https://quay.io/repository/biocontainers/ggcaller/status :target: https://quay.io/repository/biocontainers/ggcaller .. _`ggcaller/tags`: https://quay.io/repository/biocontainers/ggcaller?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/ggcaller/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/ggcaller/README.html