{% for script in extra_scripts %} {% endfor %}

Links:

File Crawler: Allows you to view all uploaded data.
Cache Status: view status of launched cellxgene servers.
{% if enable_upload %}

How To Upload Data via HTTP:

  1. Create a folder for your Username:

  2. Username
  3. Create a subdirectory under the selected Folder:


  4. Subdirectory Name
  5. Choose a folder to copy your data to, then upload your data file (must be in .h5ad format).

  6. Type in the name of the directory and subdirectory you wish to upload to, i.e. "USER/cells".
    File:

  7. Take a look at your data using the file crawler link above
{% endif %}

How To Upload Data via SSH and SCP:

  1. Confirm that your ssh key has been properly added. Running the following command should connect you to the server:
  2. ssh ec2-user@{{ ip }}
  3. Prepare your data on your own machine. They should be in a common folder called 'USER' and should look
    similar to the following structure:
  4. - USER
        - hpc.h5ad
        - pbmc3k.h5ad
  5. Copy your data to the server (replace USER with your username):
  6. ssh ec2-user@{{ ip }} 'mkdir -p {{ cellxgene_data }}/USER/'
    ssh ec2-user@{{ ip }} 'mkdir -p {{ cellxgene_data }}/USER/DATA/'
    scp -r pbmc3k.h5ad ec2-user@{{ ip }}:{{ cellxgene_data }}/USER/DATA/
  7. Take a look at your data using the file crawler link above