:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'ssdrippipeline' .. highlight: bash ssdrippipeline ============== .. conda:recipe:: ssdrippipeline :replaces_section_title: :noindex: Useful tools for the analysis of ssDRIP\-seq data :homepage: https://github.com/PEHGP/ssDripPipeline :documentation: https://github.com/PEHGP/ssDripPipeline/wiki :license: GPL3 :recipe: /`ssdrippipeline `_/`meta.yaml `_ .. conda:package:: ssdrippipeline |downloads_ssdrippipeline| |docker_ssdrippipeline| :versions: ``0.0.5-0`` :depends bedtools: ``>=2.29.2`` :depends bioconductor-deseq2: ``>=1.32.0`` :depends bioconductor-mfuzz: ``>=2.52.0`` :depends biopython: ``>=1.78`` :depends bowtie2: ``>=2.3.5.1`` :depends deeptools: ``>=3.5.0`` :depends homer: ``>=4.11`` :depends macs2: ``>=2.2.7.1`` :depends matplotlib-base: ``>=3.1.3`` :depends numpy: ``>=1.18.1`` :depends pandas: ``>=1.0.1`` :depends picard: ``>=2.24.2`` :depends python: ``>=3.7`` :depends r-base: ``>=4.1,<4.2.0a0`` :depends r-gplots: ``>=3.1.1`` :depends samtools: ``>=1.7`` :depends scipy: ``>=1.4.1`` :depends seaborn: ``>=0.10.0`` :depends ucsc-bedgraphtobigwig: :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 ssdrippipeline and update with:: mamba update ssdrippipeline To create a new environment, run:: mamba create --name myenvname ssdrippipeline 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/ssdrippipeline: (see `ssdrippipeline/tags`_ for valid values for ````) .. |downloads_ssdrippipeline| image:: https://img.shields.io/conda/dn/bioconda/ssdrippipeline.svg?style=flat :target: https://anaconda.org/bioconda/ssdrippipeline :alt: (downloads) .. |docker_ssdrippipeline| image:: https://quay.io/repository/biocontainers/ssdrippipeline/status :target: https://quay.io/repository/biocontainers/ssdrippipeline .. _`ssdrippipeline/tags`: https://quay.io/repository/biocontainers/ssdrippipeline?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/ssdrippipeline/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/ssdrippipeline/README.html