User Interface Quickstart

Learn to create a project, add members and data to the project, and run a simple workflow.

You must set up billing for your account before you can perform an analysis, or upload or egress data. Follow these instructions to set up billing.

Step 1. Create Your First Project

On the DNAnexus Platform, all data is stored within projects. So before you upload, browse, or analyze any data, you must create a project to house that data.

To create a project:

Select All Projects from the Projects link in the main menu. This will take you to the Projects page.
Click the New Project button in the top right corner of the Projects page. The New Project wizard will open in a modal window.
In the Project Name field, enter a name for your project.
In the More Info section, you can enter Tags or custom-defined Properties to make it easier to find this project later, and organize it and other projects. For more information on this topic, see this detailed explanation for more information on tags and properties.
In the More Info section, you can also enter a Project Summary and/or a Project Description.
In the Billed To field of the Billing section, choose a billing account to which project charges will be billed. Follow these instructions to set up billing.
In the Billed To field of the Billing section, choose a cloud region in which project files will be stored and analyses will be run. A default region will be displayed here; it's fine to accept this default. For more on this topic, see this detailed explanation of cloud regions.
In the Access section, specify which types of users will be able to Copy Data, Delete Data, and Download Data. Default values will be shown here; it's fine to accept the defaults. For more on project access, see this detailed explanation of project access levels. For more on types of users, see this detailed rundown.
Click Create Project. You'll be taken to the Manage screen for the project. Once you've added data to your project, this is where you'll be able to see and get info on this data, and launch analyses that use it.

Step 2. Add Project Members

Once you've created a project, you can add members by doing the following:

From the project's Manage screen, click the Share Project button - the "two people" icon - in the top right corner of the project page.
Type the username or the email address of an existing Platform user, or the ID of an org whose members you want to add the project.
In the Access pulldown, choose the type of access the user or org will have to the project. For more on this, see this detailed explanation of project access levels.
If you don't want the user to receive an email notification on being added to the project, click the Email Notification to "Off."
Click the Add User button.
Repeat Steps 2-5, for each user you want to add to the project.
Click Done when you're finished adding members.

Step 3. Add Data to Your Project

To add data to your project, click the Add button in the top right corner of the project's Manage screen. You'll see three options for adding data:

Upload Data - Use your web browser to upload data from your computer. Note that if the upload takes a significant amount of time, you'll need to ensure that until it completes, you stay logged into the Platform, and keep your browser window open.
Add Data from Server - Specify an URL of an accessible server from which the file will be uploaded.
Copy Data from Project - Copy data from another project on the Platform.

When uploading very large files, consider using the Upload Agent, a command-line tool that's both faster and more reliable than uploading via the UI.

Adding Data to Use in Your First Analysis

To prepare for running your first analysis, as detailed in Steps 4-7, copy in data from the "Demo Data" project:

From the project's Manage screen, click the Add button, then select Copy Data from Project.
In the Copy Data from Project modal window, open the "Demo Data" project by clicking on its name.
Open the "Quickstart" folder. This folder contains two 1000 Genomes project files with the paired-end sequencing reads from chromosome 20 of exome SRR100022: SRR100022_20_1.fq.gz and SRR100022_20_2.fq.gz.
Click the box next to the Name header, to select both files.
Click Copy to copy the files to your project.

Step 4. Install Apps

Next, install the apps you'll need, to analyze the data you added to the project in Step 3:

Select Tools Library from the Tools link in the main menu.
A list of available tools will open.
Find the BWA-MEM FASTQ Read Mapper in the list and click on its name.
A tool detail page will open, a full range of information about the tool, and how to use it.
Click the Install button in the upper left part of the screen, under the name of the tool.
In the Install App modal, click the Agree and Install button.
After the tool has been installed, you'll be returned to the tool detail page.
Use your browser's "Back" button to return to the tools list page.
Repeat Steps 3-6 to install the FreeBayes Variant Caller.

Step 5. Build a Workflow

Now build workflow using the two apps you've just installed, and configure it to use the data you added to your project in Step 3.

Adding Workflow Steps

A workflow runs tools as part of a preconfigured series of steps. Start building your workflow by adding steps to it:

Return to your project's Manage screen. You can do this by using your browser's "Back" button, or by selecting All Projects from the Projects link in the main menu, then clicking on the name of your project in the projects list.
Click the Add button in the top right corner of the screen, then select New Workflow from the dropdown. The Workflow Builder will open.
In the Workflow Builder, give your new workflow a name. In the upper left corner of the screen, you'll see a field with a placeholder value that begins "Untitled Workflow." Click on the "pencil" icon next to this placeholder name, then enter a name of your choosing.
Click the Add a Step button. In the Select a Tool modal window, find the BWA-MEM FASTQ Read Mapper and click the "+" to the left of its name, to add it to your workflow.
Repeat Step 4 for the FreeBayes Variant Caller.
Close the Select a Tool modal window, by clicking either on the "x" in its upper right corner, or the Close button in its lower right corner. You'll return to the main Workflow Builder screen.

Setting Inputs for Each Step

Note that in the Workflow Builder, required inputs have orange placeholder text. Optional inputs have black placeholder text.

Set the required inputs for each step by doing the following:

To set the required inputs for the first step, start by clicking on the input labeled "Reads [array]" for the BWA-MEM FASTQ Read Mapper. In the Select Data for Reads Input modal window, click the box for the SRR100022_20_1.fq.gz file. Then click the Select button.
Since the SRR100022 exome was sequenced using paired-end sequencing, you'll need to provide the right-mates for the first set of reads. Click on the input labeled "Reads (right mates) [array]" for the BWA-MEM FASTQ Read Mapper. Select the SRR100022_20_2.fq.gz file.
Click on the input labeled "BWA reference genome index." At the bottom of the modal window that opens, there will be a Suggestions section that includes a link to a folder containing reference genome files. Click on this link, then open the folder named H. Sapiens - GRCh37 - b37 (1000 Genomes Phase I). Select the human_g1k_v37.bwa-index.tar.gz file.
Next set the "Sorted mappings [array]" required input for the second step. In the "Output" section for the first step, click on the blue pill labeled "Sorted mappings," then drag it to the second step input labeled "Sorted mappings [array]."
Click on the second step input labeled "Genome." In the modal that opens, find the reference genomes folder as in Step 3. Open the folder named H. Sapiens - GRCh37 - b37 (1000 Genomes Phase I). Select the human_g1k_v37.fa.gz file.

Note that setting the inputs and outputs is different for each tool. Refer to a tool's tool detail page, in the Tools Library, to learn about its required and optional inputs and outputs, file format restrictions for each, and other information you'll need to configure it to run either on its own or as part of a workflow.

Step 6. Launch the Workflow

You're ready to launch your workflow, by doing the following:

Click the Start Analysis button at the upper right corner of the Workflow Builder.
In the modal window that opens, click the Run as Analysis button.

The BWA-MEM FASTQ Read Mapper will start executing immediately. Once it finishes, the FreeBayes Variant Caller will start, using the Read Mapper's output as an input.

Step 7. Monitor Your Job

Once you've launched your workflow, you'll be taken to your project's Monitor screen. Here, you'll see a list of both current and past analyses run within the project, along with key information about each run.

As your workflow runs, its status will be shown as "In Progress."

Terminating Your Job

If for some reason you need to terminate the run before it completes, find its row in the list on the Monitor screen. In the last column on the right, you'll see a red button labeled Terminate. Click the button to terminate the job. Note that this can take some time. While the job is being terminated, the job's status will show as "Terminating."

Step 8. Access the Results

When your workflow completes, output files will be placed into a new folder in your project, with the same name as the workflow. The folder is accessible by navigating to your project's Manage screen.

Running the Workflow Using the Full SRR100022 Exome

You can run this workflow using the full SRR100022 exome, which is available in the SRR100022 folder, in the "Demo Data" project. Note that because this entails working with a much larger file, running the workflow using the exome data will take longer.

Learn More

See these Key Concepts pages for more in-depth treatments of topics that are covered briefly here:

For a video intro to the Platform, watch this series of short, task-oriented tutorials.

For a more in-depth video intro to the Platform, watch this DNAnexus Platform Essentials video.

Last updated 5 months ago