:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bmtagger' .. highlight: bash bmtagger ======== .. conda:recipe:: bmtagger :replaces_section_title: :noindex: BMTagger aka Best Match Tagger is for removing human reads from metagenomics datasets :homepage: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/ :license: Public Domain :recipe: /`bmtagger `_/`meta.yaml `_ .. conda:package:: bmtagger |downloads_bmtagger| |docker_bmtagger| :versions: ``3.101-5``,  ``3.101-4``,  ``3.101-3``,  ``3.101-1`` :depends blast: :depends bmfilter: :depends bmtool: :depends extract_fullseq: :depends gnu-getopt: :depends srprism: :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 bmtagger and update with:: mamba update bmtagger To create a new environment, run:: mamba create --name myenvname bmtagger 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/bmtagger: (see `bmtagger/tags`_ for valid values for ````) .. |downloads_bmtagger| image:: https://img.shields.io/conda/dn/bioconda/bmtagger.svg?style=flat :target: https://anaconda.org/bioconda/bmtagger :alt: (downloads) .. |docker_bmtagger| image:: https://quay.io/repository/biocontainers/bmtagger/status :target: https://quay.io/repository/biocontainers/bmtagger .. _`bmtagger/tags`: https://quay.io/repository/biocontainers/bmtagger?tab=tags .. raw:: html Notes ----- You may find it necessary to create a bmtagger.conf file to specify paired or single\-end searching. The file should contain the line \'srprismopts\=\"\-b 100000000 \-n 5 \-R 0 \-r 1 \-M 7168\"\' along with \'\-p true\' or \'\-p false\' for paired\, and single\, respectively. This config file can be passed to bmtagger.sh via the \'\-C\' option. 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/bmtagger/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bmtagger/README.html