- recipe bmtagger
BMTagger aka Best Match Tagger is for removing human reads from metagenomics datasets
- Homepage:
- License:
Public Domain
- Recipe:
- package bmtagger¶
- Versions:
3.101-5,3.101-4,3.101-3,3.101-1- Depends:
on blast
on bmfilter
on bmtool
on extract_fullseq
on gnu-getopt
on srprism
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install bmtagger
to add into an existing workspace instead, run:
pixi add bmtagger
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install bmtagger
Alternatively, to install into a new environment, run:
conda create -n envname bmtagger
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/bmtagger:<tag>
(see bmtagger/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
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¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bmtagger/README.html)
