:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'transindel' .. highlight: bash transindel ========== .. conda:recipe:: transindel :replaces_section_title: :noindex: transIndel is used to detect indels \(insertions and deletions\) from DNA\-seq or RNA\-seq data by parsing chimeric alignments from BWA\-MEM.. :homepage: https://github.com/cauyrd/transIndel :license: GPL3 / GNU General Public License v3 or later (GPLv3+) :recipe: /`transindel `_/`meta.yaml `_ .. conda:package:: transindel |downloads_transindel| |docker_transindel| :versions: ``2.0-0``,  ``1.0-2``,  ``1.0-1``,  ``1.0-0`` :depends htseq: ``>=0.6.1`` :depends pysam: ``>=0.13.0`` :depends python: ``>=3.8`` :depends samtools: ``>=1.0`` :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 transindel and update with:: mamba update transindel To create a new environment, run:: mamba create --name myenvname transindel 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/transindel: (see `transindel/tags`_ for valid values for ````) .. |downloads_transindel| image:: https://img.shields.io/conda/dn/bioconda/transindel.svg?style=flat :target: https://anaconda.org/bioconda/transindel :alt: (downloads) .. |docker_transindel| image:: https://quay.io/repository/biocontainers/transindel/status :target: https://quay.io/repository/biocontainers/transindel .. _`transindel/tags`: https://quay.io/repository/biocontainers/transindel?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/transindel/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/transindel/README.html