- 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 bc:
- depends bedtools:
- depends biopython:
- depends blast:
- depends bowtie2:
- depends circos:
- depends gawk:
- depends mash:
>=2- depends numpy:
- depends pandas:
- depends perl-gd:
>=2.71- depends prokka:
>=1.14- depends python:
>=3.6- depends samtools:
- depends scikit-learn:
- depends scipy:
- depends spades:
- depends tabulate:
- depends tbb:
2020.2- depends trimmomatic:
- depends wget:
- requirements:
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 plasmidid and update with:: mamba update plasmidid
To create a new environment, run:
mamba create --name myenvname plasmidid
with
myenvnamebeing 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/plasmidid:<tag> (see `plasmidid/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/plasmidid/README.html)
