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Uploading Files Using Gsutil Tool

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Timothy Tickle edited this page Feb 7, 2017 · 28 revisions

Our wizard is useful if you want to upload a couple, small files into the portal. Often primary data (eg. Fastq files) are many files or big files. To upload these files, it is easier to use more appropriate tools like the gsutil tool. This tool allows you to upload files directly into your study in the cloud. This tool does require some use of command line, but we are happy to help you get acclimated to the process. Let's get started!

Getting Ready

  1. Download Gsutil Tool. The following are the official install instructions for several operating systems. If you do not have administrative rights to your system, we found the following document's instructions for installing from a tar archive very useful.

  2. Have your data (eg.fastq.gz files) in a directory you can access with a command line console (terminal program on a Mac).

  3. Get your bucket id from the portal team. Email us at single_cell_portal@broadinstitute.org and we will set up a bucket for you!

Let's Upload!

  1. Move to your directory

    cd /the/path/to/your/directory/holding/your/data

  1. Overview
  2. Creating an Account
  3. Study Creation
  4. Sharing Private Studies
  5. Visualizations Overview
  6. Creating Annotations
  7. File Definitions
  8. Uploading Data
  9. Synchronizing Study Data
  10. Search Studies
  11. Downloading Data
  12. Managing Email Notifications
  13. Running Pipelines
  14. Maintenance Window
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