:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bax2bam' .. highlight: bash bax2bam ======= .. conda:recipe:: bax2bam :replaces_section_title: :noindex: bax2bam converts the legacy PacBio basecall format \(bax.h5\) into the BAM basecall format :homepage: https://github.com/PacificBiosciences/bax2bam :license: BSD-3-Clause-Clear :recipe: /`bax2bam `_/`meta.yaml `_ .. conda:package:: bax2bam |downloads_bax2bam| |docker_bax2bam| :versions: ``0.0.11-0``,  ``0.0.9-7``,  ``0.0.9-6``,  ``0.0.9-5``,  ``0.0.9-4``,  ``0.0.9-3``,  ``0.0.9-1``,  ``0.0.9-0`` :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 bax2bam and update with:: mamba update bax2bam To create a new environment, run:: mamba create --name myenvname bax2bam 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/bax2bam: (see `bax2bam/tags`_ for valid values for ````) .. |downloads_bax2bam| image:: https://img.shields.io/conda/dn/bioconda/bax2bam.svg?style=flat :target: https://anaconda.org/bioconda/bax2bam :alt: (downloads) .. |docker_bax2bam| image:: https://quay.io/repository/biocontainers/bax2bam/status :target: https://quay.io/repository/biocontainers/bax2bam .. _`bax2bam/tags`: https://quay.io/repository/biocontainers/bax2bam?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/bax2bam/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bax2bam/README.html