Tool Library and App Introduction

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

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.

Batch analysis 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).

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

User Interface QuickStart Guide

Tool Library List

Full Documentation

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.