:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'ctseq' .. highlight: bash ctseq ===== .. conda:recipe:: ctseq :replaces_section_title: :noindex: ctSeq is a pipeline to analyze methylation patch PCR data :homepage: https://github.com/ryanhmiller/ctseq :license: MIT / MIT :recipe: /`ctseq `_/`meta.yaml `_ .. conda:package:: ctseq |downloads_ctseq| |docker_ctseq| :versions: ``0.0.2-0`` :depends bismark: :depends cutadapt: :depends ncurses: ``6.1 he6710b0_1`` :depends numpy: :depends openssl: ``1.0.2p h14c3975_1002`` :depends python: ``>=3.7`` :depends r-base: ``3.5.1.*`` :depends r-ggplot2: :depends r-pheatmap: :depends r-reshape: :depends samtools: ``1.9.*`` :depends simplesam: ``0.1.3.1.*`` :depends umi_tools: :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 ctseq and update with:: mamba update ctseq To create a new environment, run:: mamba create --name myenvname ctseq 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/ctseq: (see `ctseq/tags`_ for valid values for ````) .. |downloads_ctseq| image:: https://img.shields.io/conda/dn/bioconda/ctseq.svg?style=flat :target: https://anaconda.org/bioconda/ctseq :alt: (downloads) .. |docker_ctseq| image:: https://quay.io/repository/biocontainers/ctseq/status :target: https://quay.io/repository/biocontainers/ctseq .. _`ctseq/tags`: https://quay.io/repository/biocontainers/ctseq?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/ctseq/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/ctseq/README.html