- recipe spacerextractor
Extract CRISPR spacers from metagenome short reads.
- Homepage:
- License:
GPL3 / GPL-3.0-or-later
- Recipe:
- package spacerextractor¶
- versions:
0.9.5-0- depends bbmap:
>=39.06,<39.07- depends biopython:
>=1.78,<2- depends blast:
>=2,<3- depends bowtie:
>=1.3.1,<1.4- depends cctyper:
>=1.8,<2- depends cd-hit:
>=4.8,<4.9- depends kcounter:
>=0.1.1,<0.2- depends pandas:
>=2.0,<2.4- depends polyleven:
>=0.8,<0.9- depends pyfaidx:
>=0.8.1.3,<0.9- depends python:
- depends rich-click:
>=1.4- depends scipy:
>=1.10,<=1.11- depends seqkit:
>=2.5,<2.6- 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 spacerextractor and update with:: mamba update spacerextractor
To create a new environment, run:
mamba create --name myenvname spacerextractor
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/spacerextractor:<tag> (see `spacerextractor/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/spacerextractor/README.html)
