Academy Documentation
  • Usage of Academy Documentation
  • Getting Started
    • Background Information
    • For Apollo Users
    • For Titan Users
    • For Scientists
    • For HPC Users
    • For Experienced Users
  • Cloud Computing
    • General Information
    • Cloud Computing for Scientists
    • Cloud Computing for HPC Users
  • Overview of the Platform
    • Overview of the Platform User Interface
    • Tool Library and App Introduction
  • Billing Access and Orgs
    • Orgs and Account Management
    • Billing and Pricing
  • Cohort Browser
    • Apollo Introduction
    • Overview of the Cohort Browser
    • Combining Cohorts
    • Genomic Variant Browser
    • Somatic Variants
  • JSON
    • Introduction
    • JSON on the Platform
  • Command Line Interface (CLI)
    • Introduction to CLI
    • Advanced CLI
  • Building Applets
    • Introduction
    • Bash
      • Example 1: Word Count (wc)
      • Example 2: fastq_quality_trimmer
      • Example 3: samtools
      • Example 4: cnvkit
    • Python
      • Example 1: Word Count (wc)
      • Example 2: fastq_quality_trimmer
      • Example 3: cnvkit
  • Building Workflows
    • Native Workflows
    • WDL
      • Example 1: hello
      • Example 2: Word Count (wc)
      • Example 3: fastq_trimmer
      • Example 4: cnvkit
      • Example 5: workflow
    • Nextflow
      • Resources To Learn Nextflow
      • Overview of Nextflow
      • Nextflow Setup
      • Importing Nf-Core
      • Building Nextflow Applets
      • Error Strategies for Nextflow
      • Job Failures
      • Useful Information
  • Interactive Cloud Computing
    • Cloud Workstation
    • TTYD
    • TTYD vs Cloud Workstation
    • JupyterLab
      • Introduction
      • Running a JupyterLab Notebook
  • Docker
    • Using Docker
    • Creating Docker Snapshots
    • Running Docker with Swiss Army Knife
  • Portals
    • Overview of JSON files for Portals
    • Branding JSON File
    • Home JSON File
    • Navigation JSON File
    • Updating Your Portal
  • AI/ ML Accelerator
    • Data Profiler
      • Introduction to Data Profiler
      • Utilizing Data Profiler Navigator
      • Dataset Level Screen
      • Table Level Screen
      • Column Level Screen
      • Explorer Mode
      • Accessing Data Profiler in ML JupyterLab
    • ML JupyterLab
      • Introduction to ML JupyterLab
      • Getting Started in ML JupyterLab
      • In App Features
      • Getting Started with ML JupyterLab
    • MLflow
      • Introduction to MLflow
      • Getting Started with MLflow
      • Using MLflow Tracking Server
      • Model Registry
      • Using Existing Model
      • Utilizing MLflow in JupyterLab
Powered by GitBook
On this page
  • Tool Library
  • Running and Monitoring an App

Was this helpful?

Export as PDF
  1. Overview of the Platform

Tool Library and App Introduction

PreviousOverview of the Platform User InterfaceNextBilling Access and Orgs

Last updated 2 months ago

Was this helpful?

Before you begin, review the overview documentation and log onto the

Tool Library

The tool library is a set of ready to use apps and work flows that are maintained by DNAnexus

There are different categories and you can search by name of the tool as well

Steps to finding Tool Documentation

  1. Navigate to the Tool Library

  2. In the Any Name search box, start entering "FASTQC...."

  3. Click on the tool name, and you will be at the info tab of the tool. If you want the same version that is loaded automatically, this is all that you will need to do.

  4. If you want a different Version, to the Versions tab and select which one you are wanting

  5. Notice, you will automatically return to the Info tab for that version.

You can also select "Run" to run the app

Tool Runner Options

There are 2 options for running the tool. First, select "Run" where you find the tool documentation.

Then, there are 2 different UIs for setting up the app to run:

The guided set up, which is what you normally start with

Or, the I/O graph

Tool Useful Features

In the Stage settings tab, you can set the version of the app you want to use, instance type and specify the output folder. By specifying the instance type, you will set the computational resources of the machine on which the analysis will be run. For example, if your input data is large, you will choose an instance type with more storage space available.

Required inputs indicated by asterisks, some are optional.

It is point and click.

Can select your instance here.

Running and Monitoring an App

Set Up

  • Once you have selected the app you want to use and read the documentation (if applicable), you will use the guided setup to run the app in the UI.

  • Set the Output folder

  • Set the inputs. In the example of FASTQC, it is one FASTQ file

  • Launch the app using the start analysis button in the upper right

  • You will have a review step. This is to review the content as well as add additional parameters such as a spending limit.

Monitor An App

  • You will automatically be redirected to the monitor page

  • When the job is completed, you will have buttons to access the inputs (such as a FASTQ file) and outputs (such as an HTML file).

  • Here is the view when the app is completed:

Supplemental Information

Using Apps in the GUI

Batch Processing in the GUI

Monitoring An App/ Workflow

Resources

To create a support ticket if there are technical issues:

  1. Go to the Help header (same section where Projects and Tools are) inside the platform

  2. Select "Contact Support"

  3. Fill in the Subject and Message to submit a support ticket.

can be enabled here. At this time, the feature applies to a batch of inputs. The output is aggregated in one output file. (e.g. 10 inputs results in 1 output).

Batch analysis
User Interface QuickStart Guide
Tool Library List
Full Documentation
DNAnexus Platform