Example and tutorial

Engine-initiated local analysis

  1. Install MARTi (Engine and GUI) by following the steps on the Download and installation page.

  2. Once installed, download the example reads, custom database, and taxonomy files from here.

  3. Extract the downloaded files and navigate to the config directory. Open marti_test.txt with a text editor and replace /usr with the path to your unzipped marti_example directory.

  4. Open ~/marti_engine_options.txt in a text editor and update the TaxonomyDir, MinKNOWRunDirectory, and MARTiSampleDirectory paths (replacing /path/to/marti_example/ with the actual path to your unzipped marti_example directory):

    TaxonomyDir:/path/to/marti_example/databases/taxonomy_6Jul20
MinKNOWRunDirectory:/path/to/marti_example/reads
MARTiSampleDirectory:/path/to/marti_example/output

  5. Open a terminal in the marti_example directory and run the MARTi Engine with the following command:

    marti -config config/marti_test.txt

  6. Open another terminal window and launch the MARTi GUI by running marti_gui, then open a browser and navigate to localhost:3000.

  7. The marti_test sample should appear in the sample selection table. View the results in the Dashboard by clicking on the Sample ID.

Docker - GUI-initiated local analysis

The following steps will take you through a local MARTi analysis of a small set of nanopore reads from the Zymo Microbial Mock Community using the docker image.

  1. A docker image of MARTi, which includes all of the required dependencies, is provided on Docker Hub. To get started, ensure that you have installed the Docker Engine on your system.

  2. Once installed, you can pull the MARTi image by running the following command:

    docker pull nedpeel/marti

  3. Download the sample reads, custom database, and taxonomy files from here.

  4. Unzip the downloaded files and run the MARTi Docker image with the following command (replacing /path/to/marti_example/ with the actual path to the unzipped marti_example directory):

    docker run -i -t -p 3000:3000 -v /path/to/marti_example/databases:/usr/databases -v /path/to/marti_example/reads:/usr/reads -v /path/to/marti_example/output:/usr/output nedpeel/marti

  5. Launch the MARTi GUI by running marti_gui in the docker terminal, then open a browser and navigate to GUI’s port localhost:3000.

  6. Navigate to the “New analysis” page using the navbar on the lefthand side of the page.

  7. Make sure that the Zymo mock data directory is selected in the Input data directory dropdown.

  8. In the Analysis processes section further down the page, check the zymo_mock option to add a blast process to the custom zymo database.

  9. Scroll to the bottom of the page and click Start analysis to initiate the MARTi Engine.

  10. 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.