jimmlucas/ariba repository overview

Docker image for ARIBA (Antimicrobial Resistance Identification By Assembly), built from the fork jimmlucas/ariba⁠, branch [fix-pubmlst-db-error[(https://github.com/sanger-pathogens/ariba/pull/345⁠).

This image includes a fix for PubMLST database generation (updated pubmlst_getter.py to correctly handle per-gene .tfa files), and bundles all required dependencies to run ARIBA for antimicrobial resistance detection and genotype/MLST profiling from sequencing reads.

The image installs:

• ARIBA from the forked source code

• Bioinformatics dependencies: bowtie2, SPAdes, cd-hit, mummer, etc.

• Python dependencies from requirements.txt

Basic usage

Show help:

docker run --rm -it jimmlucas/ariba:V1.2.0 ariba -h

Show ARIBA version:

docker run --rm -it jimmlucas/ariba:V1.2.0 ariba version

Notes

• The image is intended for workflows using ARIBA with PubMLST databases, benefiting from the bugfix in the PubMLST getter logic.

• Use -v to mount input and output directories from the host so that results are persisted outside the container.