:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'gap2seq' .. highlight: bash gap2seq ======= .. conda:recipe:: gap2seq :replaces_section_title: :noindex: Gap2Seq is a tool for filling gaps between contigs in genome assemblies. :homepage: https://www.cs.helsinki.fi/u/lmsalmel/Gap2Seq/ :license: GPLv3 :recipe: /`gap2seq `_/`meta.yaml `_ .. conda:package:: gap2seq |downloads_gap2seq| |docker_gap2seq| :versions: .. raw:: html
3.1.1a-23.1.1a-13.1.1a-03.1-33.1-23.1-13.1-02.1-42.1-3 ``3.1.1a-2``,  ``3.1.1a-1``,  ``3.1.1a-0``,  ``3.1-3``,  ``3.1-2``,  ``3.1-1``,  ``3.1-0``,  ``2.1-4``,  ``2.1-3``,  ``2.1-2``,  ``2.1-1``,  ``2.1-0``,  ``2.0-8``,  ``2.0-7``,  ``2.0-6``,  ``2.0-5``,  ``2.0-4``,  ``2.0-1`` .. raw:: html
:depends htslib: ``>=1.17,<1.20.0a0`` :depends libgcc-ng: ``>=12`` :depends libstdcxx-ng: ``>=12`` :depends python: ``>=3.10,<3.11.0a0`` :depends python_abi: ``3.10.* *_cp310`` :depends zlib: :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 gap2seq and update with:: mamba update gap2seq To create a new environment, run:: mamba create --name myenvname gap2seq 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/gap2seq: (see `gap2seq/tags`_ for valid values for ````) .. |downloads_gap2seq| image:: https://img.shields.io/conda/dn/bioconda/gap2seq.svg?style=flat :target: https://anaconda.org/bioconda/gap2seq :alt: (downloads) .. |docker_gap2seq| image:: https://quay.io/repository/biocontainers/gap2seq/status :target: https://quay.io/repository/biocontainers/gap2seq .. _`gap2seq/tags`: https://quay.io/repository/biocontainers/gap2seq?tab=tags .. raw:: html Notes ----- Gap2Seq is only tested on Linux x86\_64 by its author. 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/gap2seq/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/gap2seq/README.html