Example and tutorial

Engine-initiated local analysis

Install MARTi (Engine and GUI) by following the steps on the Download and installation page.
Once installed, download the example reads, custom database, and taxonomy files from here.
Extract the downloaded files and navigate to the config directory. Open marti_test.txt with a text editor and replace all occurrences of /usr with the path to your unzipped marti_example directory.
Open a terminal in the marti_example directory and run the MARTi Engine with the following command:
```
marti -config config/marti_test.txt
```
Open another terminal window and launch the MARTi GUI with the following command. Be sure to replace /path/to/output with the actual path to the output directory inside your unzipped marti_example directory:
```
marti_gui --marti /path/to/output
```
Open a browser and navigate to localhost:3000
The marti_test sample should appear in the sample selection table. View the results in the Dashboard by clicking on the Sample ID.

The following steps will take you through a local MARTi analysis initiated from the GUI.

Install MARTi (Engine and GUI) by following the steps on the Download and installation page.
Once installed, download the example reads, custom database, and taxonomy files from here.
Extract the downloaded files.
Open a terminal window and run the MARTi GUI with the following command. Be sure to replace /path/to/ with the full paths to directories inside your unzipped marti_example directory:
```
marti_gui --marti /full/path/to/output --taxonomy /full/path/to/databases/taxonomy_6Jul20 --minknow /full/path/to/reads
```
Launch the MARTi GUI by running marti_gui in a terminal, then open a browser and navigate to GUI’s port localhost:3000.
Navigate to the “New analysis” page using the navbar on the lefthand side of the page.
Make sure that the Zymo mock data directory is selected in the Input data directory dropdown.
In the Analysis processes section further down the page, check the example option to add a blast process. Replace the Database path with the actual path to the custom zymo database. The process should look something like this:
```
Name:example_blast
Program:megablast
Database:/full/path/to/databases/zymo_mock/zymo_refs_sam.fasta
MaxE:0.001
MaxTargetSeqs:25
UseToClassify
```
Scroll to the bottom of the page and click Start analysis to initiate the MARTi Engine.
At this point you should automatically be redirected to the Samples page. Within a minute or two the Zymo sample will appear in the sample selection table.