- recipe plasmidid
Pipeline for plasmid identification and reconstruction
- Homepage:
- License:
GPLv3
- Recipe:
PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.
- package plasmidid¶
- Versions:
1.6.5-0,1.6.4-3,1.6.4-2,1.6.4-1,1.6.4-0,1.6.3-2,1.6.3-1,1.6.3-0,1.6.2-0,1.6.5-0,1.6.4-3,1.6.4-2,1.6.4-1,1.6.4-0,1.6.3-2,1.6.3-1,1.6.3-0,1.6.2-0,1.6.0-0,1.5.2-0- Depends:
on bc
on bedtools
on biopython
on blast
on bowtie2
on circos
on gawk
on mash
>=2on numpy
on pandas
on perl-gd
>=2.71on prokka
>=1.14on python
>=3.6on samtools
on scikit-learn
on scipy
on spades
on tabulate
on tbb
2020.2on trimmomatic
on wget
- 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 plasmidid
to add into an existing workspace instead, run:
pixi add plasmidid
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 plasmidid
Alternatively, to install into a new environment, run:
conda create -n envname plasmidid
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/plasmidid:<tag>
(see plasmidid/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/plasmidid/README.html)
