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Frequently Asked Questions

Account Questions
Where can I find the Terms of Service or the Privacy Policy?
How can I sign up for updates when new data or features are added to the cloud?
How can I delete my account?

Billing Questions
Will I be charged for using St. Jude Cloud?
How can I set up billing for my lab?

Data Request Questions
Why do I need to sign the Data Access Agreement (DAA)?
Can I make edits/revisions to the DAA?
Can I get a Microsoft Word version of the DAA
Where can I find the latest version of the Data Access Agreement (DAA)?
Where do I submit the Data Access Agreement (DAA)?
What if I did not fill out the Data Download Permission section of the original DAA, but now I want to download data?
What clinical information is available about samples in St. Jude Cloud?
Can I get a copy of IRB consent forms?
Can I request FASTQ files on St. Jude Cloud?

Technical Questions
How can I explore and manipulate data files stored on the cloud without downloading the files to my local machine?
How can I run an analysis workflow on multiple sample files at the same time?
How can I connect to DNAnexus API via SSH on a Windows machine?
Why am having trouble connecting to DNAnexus API via SSH?

Publication Questions
How do I cite St. Jude Cloud?
When can I publish my findings using St. Jude Cloud data?
Where can I find the embargo date?

Miscellaneous
Will St. Jude Cloud host my institution's data in the data browser or on PeCan?

Where can I find the Terms of Service or the Privacy Policy?

You can find the Terms of Service here and the Privacy Policy here.

How can I sign up for updates when new data or features are added to the cloud?

We are always adding data to St. Jude Cloud, and if you would like to sign up for updates, subscribe here.

How can I delete my account?

If you'd like to delete your account, please email DNAnexus support at support@dnanexus.com with the following email.

Hi DNAnexus,

  Would you please assist me in deleting my St. Jude Cloud account? My username is _____.

Thank you!

Will I be charged for using St. Jude Cloud?

Any copy of the St. Jude data you receive is considered "sponsored", so you do not have to pay a fee to store this data in St. Jude Cloud. Although you may be prompted to enter billing information, you will not be charged for anything with the exception of the following actions:

  • You will be charged for any derivative files stored on the St. Jude Cloud, such as results files obtained through running analyses workflows.
  • There is a small monthly storage fee associated for any of your own data you upload to the cloud.
  • If you elect to download any data from St. Jude Cloud, you will be charged an egress fee by DNAnexus. This fee is usually negligible unless you are downloading entire cohorts. We are actively investigating ways to minimize or eliminate these costs.
  • If you run any of our analysis workflows (such as Rapid RNA-Seq, WARDEN, etc.) or your own workflows that you have uploaded and packaged into the cloud, you will be charged for the compute resources used in producing the results. Soon we hope to be able to sponsor all compute costs associated with running our St. Jude Cloud workflows.

You can find DNAnexus's specific resource-based pricing table by navigating to the Billing Account tab of your profile page on DNAnexus and then clicking the green 'Add Billing Info' button next to your name.

How can I set up billing for my lab?

Billing setup is different based on whether you are an internal user (you work at St. Jude) or an external user. External users refer to the Create an Account page for instructions. Internal users search 'Bioinformatics self-service on St. Jude Cloud' from the intranet home page for instructions.

Why do I need to sign the Data Access Agreement (DAA)?

Although the DAA serves many purposes, the terms included in the data access agreement are ultimately in place to protect our patients. We take patient security very seriously, and we require that requesters are committed to protecting that privacy to the fullest extent.

Can I make edits/revisions to the DAA?

As a rule, we do not negotiate the terms of the data access agreement unless terms are found to be in conflict with the institution's state law. The terms included in the data access agreement are ultimately in place to protect our patients, a matter which we take very seriously.

Can I get a Microsoft Word version of the DAA?

No. If we provide an editable format, we cannot ensure that the legal document has not been changed. Since we do not accept different versions of this agreement, we unfortunately cannot provide the document in Word format.

Where can I find the latest version of the Data Access Agreement (DAA)?

We keep our site up to date with the latest version on the Data Access Agreement for you to download, or you can download a copy here.

Where do I submit the Data Access Agreement (DAA)?

You can submit your Data Access Agreement in the drag and drop box on the last step of the data request process.

What if I did not fill out the Data Download Permission section of the original DAA, but now I want to download data?

Since this would be a change in terms from the original agreement, you would need to fill out a new DAA (including the Data Download Permission section for any datasets you want to download.

What clinical information is available about samples in St. Jude Cloud?

Currently the only clinical information we provide is age at diagnosis, diagnosis, ethnicity, sex, race, and oncotree disease code. Unfortunately, even if we do collect other information, such as other supportive oncology data, it is not available on the cloud at this time. We are working towards being able to provide additional clinical annotations in the future.

Unfortunately, we will not be able to share blank consent forms at the current time. We have chosen to remain consistent with the requirements of the other major genomic data repositories in that (1) there is an internal vetting process by the St. Jude IRB to ensure samples may be shared with the research community, but (2) we do not share the informed consents with data requesters. It is important to remember that St. Jude Cloud is the platform upon which all St. Jude data is shared. This means that there are more than 100 consent forms + revisions for the various studies across St. Jude. Thus, there is an additional logistical barrier in that we simply don't have the bandwidth to pull together a packet containing all of this information for each requestor.

Can I request FASTQ files on St. Jude Cloud?

We do not share FASTQ formats, but several tools exist that you can leverage to revert BAM to FASTQ files. (We recommend using Picard SamToFastq to revert BAM files.) You can efficiently revert BAMs to FASTQs in the cloud by wrapping the conversion tool of your choice into a Cloud App.

How can I explore and manipulate data files stored on the cloud without downloading the files to my local machine?

You can quickly and easily interact with data files using the DNAnexus cloud workstation app. See this guide to help you setup and run the app. Note that if you are doing any type of large-scale, multi-sample analysis, espescially if you plan to repeat the analysis or want to run in parallel, you will want to write your own cloud app rather than use the cloud workstation app.

How can I run an analysis workflow on multiple sample files at the same time?

The DNAnexus interface does have a batch tool available; however, it is in early testing, so we recommend using dx-toolkit on the command line as the most reliable and user friendly approach to batch and submit jobs. You can find our documentation on how to install and get started with dx-toolkit here. You may also refer to the sample script below that loops through all the BAM files in the data folder and submits a job using the BAM and matching index file.

for bam in $(dx ls '/data/*.bam'); do  
  dx run \  
    --yes \  
    --input "0.BAM=/data/$bam" \
    --input "0.BAM_INDEX=/data/$bam.bai" \
    "$PROJECT_ID:/Rapid RNA-Seq (BAM)"
done

Note that this sample script assumes that the BAM and index files are in the data folder and the Rapid RNA-Seq analysis workflow is in the project. $PROJECT_ID can be set to your project dxid, and Rapid RNA-Seq (BAM) can be changed to the workflow you want to run.

How can I connect to DNAnexus API via SSH on a Windows machine?

To connect via SSH on a Windows machine we recommend using Windows Subsystem for Linux (WSL) or a Linux virtual machine.
The WSL method:
1. Open PowerShell as an administrator and run
Enable-WindowsOptionalFeature -Online -FeatureName Microsoft-Windows-Subsystem-Linux
2. Restart computer.
3. Install Ubuntu from the Microsoft Store.
4. Open Ubuntu. This prompts you to create a user and password.
5. Install dx toolkit:
$ sudo apt update
$ sudo apt install python-minimal python-pip
$ pip install dxpy
6. Close Ubuntu window. Open Ubuntu again.
7. Log in to DNAnexus, where $TOKEN is an API Token.
$ dx login --token $TOKEN

You may also find these instructions on the DNAnexus documentation helpful.

Why am I getting a connectivity error when connecting to DNAnexus API via SSH?

If you are trying to run something like
$ dx run --ssh <executable>
and are getting a connectivity error, it may be that your firewall is too restrictive. Are you able to perform the command from an unrestricted network (like a home network)? If yes, you can resolve this issue by asking your network administrator to whitelist connections to Azure US West. All subnets (Region Name="uswest") are provided here.

How do I cite St. Jude Cloud?

We are currently in progress of preparing a paper for St. Jude Cloud. In the meantime, please refer to the citation table on the Welcome page.

When can I publish my findings using St. Jude Cloud data?

Once the embargo date for the St. Jude datasets that you've used in your research has passed, you are legally permitted to publish results based on that data.

Where can I find the embargo date?

All of our samples are marked with an embargo date. You can find this by looking at the tags for each file or in the SAMPLE_INFO.txt file that is included with each data request. Select a sample and click info to see more.

Will St. Jude Cloud host my institution's data in the data browser or on PeCan?

If you are interested in submitting data to St. Jude Cloud, please contact us at support@stjude.cloud.