:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'discasm' .. highlight: bash discasm ======= .. conda:recipe:: discasm :replaces_section_title: :noindex: DISCASM aims to extract reads that map to reference genomes in a discordant fashion and optionally include reads that do not map to the genome at all\, and perform a de novo transcriptome assembly of these reads. DISCASM relies on the output from STAR \(as run via STAR\-Fusion\)\, and supports de novo transcriptome assembly using Trinity or Oases. \- https\:\/\/github.com\/DISCASM\/DISCASM\/wiki :homepage: https://github.com/DISCASM/DISCASM :license: BSD-3-Clause :recipe: /`discasm `_/`meta.yaml `_ .. conda:package:: discasm |downloads_discasm| |docker_discasm| :versions: ``0.1.3-1``,  ``0.1.3-0``,  ``0.1.2-2``,  ``0.1.2-1``,  ``0.1.2-0`` :depends oases: ``>=0.2`` :depends perl: :depends pysam: ``>=0.10.0`` :depends python: ``<3`` :depends star: ``>=2.4`` :depends trinity: ``>=2.4`` :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 discasm and update with:: mamba update discasm To create a new environment, run:: mamba create --name myenvname discasm 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/discasm: (see `discasm/tags`_ for valid values for ````) .. |downloads_discasm| image:: https://img.shields.io/conda/dn/bioconda/discasm.svg?style=flat :target: https://anaconda.org/bioconda/discasm :alt: (downloads) .. |docker_discasm| image:: https://quay.io/repository/biocontainers/discasm/status :target: https://quay.io/repository/biocontainers/discasm .. _`discasm/tags`: https://quay.io/repository/biocontainers/discasm?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/discasm/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/discasm/README.html