:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'transposcope' .. highlight: bash transposcope ============ .. conda:recipe:: transposcope :replaces_section_title: :noindex: A package for visualizing read coverage in areas flanking mobile element insertions. :homepage: https://github.com/FenyoLab/transposcope :license: MIT / MIT License :recipe: /`transposcope `_/`meta.yaml `_ .. conda:package:: transposcope |downloads_transposcope| |docker_transposcope| :versions: ``2.0.1-0``,  ``2.0.0-1``,  ``2.0.0-0``,  ``0.1.2-0``,  ``0.1.0-0`` :depends biopython: ``>=1.76`` :depends bowtie2: ``>=2.3.5`` :depends numpy: ``>=1.17.4`` :depends pandas: ``>=0.25.1`` :depends pysam: ``>=0.15.3`` :depends python: ``>=3`` :depends samtools: ``>=1.10`` :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 transposcope and update with:: mamba update transposcope To create a new environment, run:: mamba create --name myenvname transposcope 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/transposcope: (see `transposcope/tags`_ for valid values for ````) .. |downloads_transposcope| image:: https://img.shields.io/conda/dn/bioconda/transposcope.svg?style=flat :target: https://anaconda.org/bioconda/transposcope :alt: (downloads) .. |docker_transposcope| image:: https://quay.io/repository/biocontainers/transposcope/status :target: https://quay.io/repository/biocontainers/transposcope .. _`transposcope/tags`: https://quay.io/repository/biocontainers/transposcope?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/transposcope/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/transposcope/README.html