:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'hicup' .. highlight: bash hicup ===== .. conda:recipe:: hicup :replaces_section_title: :noindex: A tool for mapping and performing quality control on Hi\-C data :homepage: http://www.bioinformatics.babraham.ac.uk/projects/hicup/ :license: GPLv3 :recipe: /`hicup `_/`meta.yaml `_ :links: biotools: :biotools:`hicup`, doi: :doi:`10.12688/f1000research.7334.1` .. conda:package:: hicup |downloads_hicup| |docker_hicup| :versions: .. raw:: html
0.9.2-10.9.2-00.8.3-10.8.3-00.8.2-00.8.1-00.7.3-10.7.3-00.7.2-0 ``0.9.2-1``,  ``0.9.2-0``,  ``0.8.3-1``,  ``0.8.3-0``,  ``0.8.2-0``,  ``0.8.1-0``,  ``0.7.3-1``,  ``0.7.3-0``,  ``0.7.2-0``,  ``0.6.1-1``,  ``0.6.1-0``,  ``0.5.10-0``,  ``0.5.9-0`` .. raw:: html
:depends bowtie: :depends bowtie2: :depends pandoc: :depends perl: :depends perl-bioperl: :depends r-base: :depends r-plotly: :depends r-rmarkdown: :depends r-stringi: ``>=1.7.8`` :depends r-tidyverse: :depends samtools: :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 hicup and update with:: mamba update hicup To create a new environment, run:: mamba create --name myenvname hicup 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/hicup: (see `hicup/tags`_ for valid values for ````) .. |downloads_hicup| image:: https://img.shields.io/conda/dn/bioconda/hicup.svg?style=flat :target: https://anaconda.org/bioconda/hicup :alt: (downloads) .. |docker_hicup| image:: https://quay.io/repository/biocontainers/hicup/status :target: https://quay.io/repository/biocontainers/hicup .. _`hicup/tags`: https://quay.io/repository/biocontainers/hicup?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/hicup/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/hicup/README.html