recipe bmtagger

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

package bmtagger

(downloads) 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:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see 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:<tag>

(see `bmtagger/tags`_ for valid values for ``<tag>``)

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.

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