Run the full mbX Pro 16S pipeline from the terminal with no setup. Docker, QIIME2, R, Python and the analysis image are all bundled here — you do not install anything.

What's in this folder

cli/
├── mbXPro            ← the launcher you call
├── run_demo.sh       ← one-shot: runs the pipeline on the test data set
├── engine/           ← container glue script (do not edit)
└── payload/          ← bundled runtime + 4.2 GB analysis image (do not edit)

The test data lives one level up, in ../test_data_set/.

Quick start (run the test data set)

Open Terminal, drag this cli folder onto the Terminal icon (or cd into it), then run:

./run_demo.sh

That's it. It boots the analysis engine once, then runs the complete pipeline on the bundled test samples. When it finishes, your results are in:

demo_outputs/mbX_pro_outputs_<timestamp>/

Open the report:

open demo_outputs/mbX_pro_outputs_*/18_final_report/mbX_pro_final_report.html

Running your own data

The simplest form — just give it your FASTQ folder and metadata file:

./mbXPro /path/to/your/FASTQ_folder /path/to/your/metadata.txt

Results are written next to your FASTQ folder, in a timestamped mbX_pro_outputs_<date>/ folder. You can also choose where they go by adding an output folder as a third argument:

./mbXPro /path/to/FASTQ /path/to/metadata.txt /path/to/output_location

That's all most users need — nothing to install. The first run boots the analysis engine (VM + image load) automatically.

Advanced (subcommands)

./mbXPro run \
    --fastq    /path/to/your/FASTQ_folder \
    --metadata /path/to/your/metadata.txt \
    --out      /path/to/output_location

./mbXPro prepare   # just boot the VM + load the image
./mbXPro stop      # shut the engine down to free RAM
./mbXPro doctor    # print readiness

Note: the FASTQ folder, metadata file, and output location must all be inside your home folder (Desktop, Documents, etc.).

Pass extra mbX Pro flags after a --, e.g. publication-quality figures:

./mbXPro /path/to/FASTQ /path/to/metadata.txt -- --publication-figures

Troubleshooting

• "cannot be opened because it is from an unidentified developer" — the launcher already clears that flag for the bundled files. If macOS still blocks a binary, run once: xattr -dr com.apple.quarantine .
• Want to start completely fresh? ./mbXPro stop then delete ~/.mbxpro.