:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'ls-gkm' .. highlight: bash ls-gkm ====== .. conda:recipe:: ls-gkm :replaces_section_title: :noindex: gkm\-SVM\, a sequence\-based method for predicting regulatory DNA elements\, is a useful tool for studying gene regulatory mechanisms. In continuous efforts to improve the method\, new software\, LS\-GKM\, is introduced. It offers much better scalability and provides further advanced gapped k\-mer based kernel functions. As a result\, LS\-GKM achieves considerably higher accuracy than the original gkm\-SVM. :homepage: https://github.com/Dongwon-Lee/lsgkm :license: GPL3 :recipe: /`ls-gkm `_/`meta.yaml `_ .. conda:package:: ls-gkm |downloads_ls-gkm| |docker_ls-gkm| :versions: ``0.0.1-1``,  ``0.0.1-0`` :depends libstdcxx-ng: ``>=4.9`` :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 ls-gkm and update with:: mamba update ls-gkm To create a new environment, run:: mamba create --name myenvname ls-gkm 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/ls-gkm: (see `ls-gkm/tags`_ for valid values for ````) .. |downloads_ls-gkm| image:: https://img.shields.io/conda/dn/bioconda/ls-gkm.svg?style=flat :target: https://anaconda.org/bioconda/ls-gkm :alt: (downloads) .. |docker_ls-gkm| image:: https://quay.io/repository/biocontainers/ls-gkm/status :target: https://quay.io/repository/biocontainers/ls-gkm .. _`ls-gkm/tags`: https://quay.io/repository/biocontainers/ls-gkm?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/ls-gkm/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/ls-gkm/README.html