:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'imfusion' .. highlight: bash imfusion ======== .. conda:recipe:: imfusion/0.3.2 :replaces_section_title: :noindex: IM\-Fusion \- Tool for identifying transposon insertions and their effects from RNA\-sequencing data :homepage: https://github.com/jrderuiter/imfusion :license: MIT :recipe: /`imfusion `_/`0.3.2 `_/`meta.yaml `_ .. conda:package:: imfusion |downloads_imfusion| |docker_imfusion| :versions: ``0.3.2-0``,  ``0.3.0-0`` :depends bowtie: :depends future: :depends htseq: ``>=0.7.2`` :depends htslib: ``<1.4`` :depends intervaltree: :depends intervaltree: :depends matplotlib: :depends numexpr: :depends pandas: :depends pathlib2: :depends pyfaidx: ``>=0.4.8.1`` :depends pysam: ``>=0.9.1`` :depends python: ``2.7*`` :depends scipy: :depends seaborn: :depends seaborn: :depends star: :depends stringtie: :depends subread: :depends toolz: :depends tophat: ``>=2.1.0`` :depends typing: :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 imfusion and update with:: mamba update imfusion To create a new environment, run:: mamba create --name myenvname imfusion 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/imfusion: (see `imfusion/tags`_ for valid values for ````) .. |downloads_imfusion| image:: https://img.shields.io/conda/dn/bioconda/imfusion.svg?style=flat :target: https://anaconda.org/bioconda/imfusion :alt: (downloads) .. |docker_imfusion| image:: https://quay.io/repository/biocontainers/imfusion/status :target: https://quay.io/repository/biocontainers/imfusion .. _`imfusion/tags`: https://quay.io/repository/biocontainers/imfusion?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/imfusion/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/imfusion/README.html