Manage Your Data

Last updated: 2 years ago (view history), Time to read: 2 mins

In this section, you will learn how and where to find your data so that you can use our visualization editors.

tip
  • The key is case in-sensitive.
  • Dropbox storage url keys will not work since these are binary files.
  • Amazon (AWS) and DNAnexus are two examples that runproteinpaint() can access.
  • The key is only for internal St. Jude users to access the HPC within the directory.

Follow the below tutorials if you want to upload data to DNAnexus:

  • if you have your data stored in DNAnexus, go here.
  • if you have your data stored on your local and want to upload to DNAnexus, go here.
warning

You must follow the below tutorial to extend your links after you upload your data. Otherwise, the links in DNAnexus are available for 24h only and therefore your visualization will not render after that allotted time.

Accessing DNAnexus from the command line (to extend your file duration)

First, you will want to check if you have python installed.

python --version

Then, check if you have python3 installed

python3 --version

now install DNAnexus.

pip3 install dxpy

Open DNAnexus to ensure you can access it from the command line.

dx

Get your token by logging into DNAnexus. Navigate to your profile icon. Select the API token in the top navbar. Select to generate the token. Then go to your terminal and enter:

dx login --token add_token_here

Pick a project to enter and then type the below to see all files in that project.

dx ls

You can type the below to see the durations.

dx make_download_url file_name.txt --help

Now, set your duration. 

dx make_download_url file_name.txt --duration 100y

Use the new URL as VisCom’s url key, be sure to save this to reference later.

Accessing the HPC

  • If you have your data stored on the HPC and want to move it to DNAnexus, follow these instructions.

  • In order to allow ProteinPaint’s server to access your data on the HPC, you must move it to to the directory. To access this, signin (see this tutorial) and type 

    cd /research/rgs01/resgen/legacy/gb_customTracks/tp

Here, you can make a new directory to store your data.

tip

The data must be on the proteinpaint.stjude.org server and not ppr1, otherwise your visualizations have to be viewed by VPN.