- recipe smeg
Strain-level Metagenomic Estimation of Growth rate (SMEG) measures growth rates of microbial strains from complex metagenomic dataset
- Homepage:
- License:
MIT
- Recipe:
- package smeg¶
- Versions:
1.1.5-2,1.1.5-1,1.1.5-0,1.1.4-1,1.1.4-0,1.1.3-0,1.1.2-0,1.1.1-0,1.1-1,1.1.5-2,1.1.5-1,1.1.5-0,1.1.4-1,1.1.4-0,1.1.3-0,1.1.2-0,1.1.1-0,1.1-1,1.1-0,1.0.1-2,1.0.1-1,1.0.1-0- Depends:
on bamtools
on bedtools
on blast
on bowtie2
on libgenome
on mauve
on openssl
>=1.1.0,<=1.1.1on parallel
on prokka
on r-ape
on r-data.table
on r-dplyr
on r-dynamictreecut
on r-getopt
on r-ggplot2
on r-gplots
on r-gsubfn
on r-seqinr
on readline
>=6.2on roary
on samtools
- 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 smeg
to add into an existing workspace instead, run:
pixi add smeg
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 smeg
Alternatively, to install into a new environment, run:
conda create -n envname smeg
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/smeg:<tag>
(see smeg/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.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/smeg/README.html)
