recipe rgi

This tool provides a preliminary annotation of your DNA sequence(s) based upon the data available in The Comprehensive Antibiotic Resistance Database (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will be highlighted. As CARD expands to include more pathogens, genomes, plasmids, and ontology terms this tool will grow increasingly powerful in providing first-pass detection of antibiotic resistance associated genes. See license at CARD website

Homepage:

https://card.mcmaster.ca

License:

https://card.mcmaster.ca/about

Recipe:

/rgi/meta.yaml

Links:

doi: 10.1093/nar/gkz935

package rgi

versions:

6.0.3-1,  6.0.3-0,  6.0.2-0,  6.0.1-1,  6.0.1-0,  6.0.0-0,  5.2.1-2,  5.2.1-1,  5.2.1-0, 

6.0.3-1,  6.0.3-0,  6.0.2-0,  6.0.1-1,  6.0.1-0,  6.0.0-0,  5.2.1-2,  5.2.1-1,  5.2.1-0,  5.2.0-0,  5.1.1-0,  5.1.0-1,  5.1.0-0,  5.0.0-0,  4.2.2-1,  4.2.2-0,  4.0.3-3,  4.0.3-2,  4.0.3-1,  4.0.3-0,  3.2.1-4,  3.2.1-3,  3.2.1-2,  3.2.1-1,  3.2.0-3,  3.2.0-2,  3.2.0-1,  3.1.2-3,  3.1.2-2,  3.1.2-1,  3.1.1-2,  3.1.1-1,  3.1.0-1,  3.1.0-0

depends bamtools:

>=2.5.1,<2.5.2.0a0

depends beautifulsoup4:

4.9.3

depends bedtools:

>=2.28.0

depends biopython:

1.78.*

depends blast:

>=2.9.0

depends bowtie2:

>=2.3.4.3

depends bwa:

>=0.7.17

depends dask:

depends diamond:

0.8.36.*

depends filetype:

>=1.0.0

depends kma:

>=1.2.26

depends lxml:

4.6.5

depends matplotlib-base:

>=2.1.2

depends oligoarrayaux:

3.8.*

depends pandas:

>=0.15.0

depends prodigal:

2.6.3.*

depends pyahocorasick:

>=1.1.7

depends pyfaidx:

>=0.5.4.1

depends pyrodigal:

>=2.0.0,<3

depends pysam:

0.16.0.1

depends python:

>=3.5

depends requests:

2.24.0

depends samtools:

1.9.*

depends seaborn:

>=0.8.1

depends six:

>=1.7.0

depends wget:

depends zlib:

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 rgi

and update with::

   mamba update rgi

To create a new environment, run:

mamba create --name myenvname rgi

with myenvname being 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/rgi:<tag>

(see `rgi/tags`_ for valid values for ``<tag>``)

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