AWS_smrt_portal_directions

Amazon Web Services and SMRT Portal
1) Sign into AWS, restart "instance".  
    ****If this is the first time you are creating an instance in AWS, follow steps here, including downloading permissions file (.pem): https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/%22Installing%22-SMRT-Portal-the-easy-way---Launching-A-SMRT-Portal-AMI

2) From command line (on your computer) upload new data (smrt cells):
        scp  -r -i /path/to/your/permissions_file.pem /path/to/your/smrt_cells  ubuntu@##########:/opt/smrtanalysis/userdata/inputs_dropbox
        Where ########## is your public DNS from AWS instance (this often has to be refreshed every time you log into AWS)

3) Sign into SMRTPortal with new "instance" address:  http://##########:8080/smrtportal
        Where ########## is your public DNS from AWS instance

4) In SMRTPortal, go to "Home" or "Design Job" --> "Import and Manage"

      You should now see your SMRT cells there, click "Import SMRTcells"
      Click "Scan"
      Then "Add"  (you don't need a path)
      
5) Go to "Design Job" --> "Create New"
      Enter a name
      Select protocol to use for this job e.g. RS_HGAP_Assembly.2, or RS_ReadsofInsert.1
      Change any settings or parameters (e.g. "Barcode.1.xml", "Remove control sequences" in Protocol Parameter, threshold for how many reads are needed to keep them in output, or length cutoffs, etc.)
      Add SMRTcell(s) to analyze with "play" button
      Click "save" to save for later
      Click "start" to start

Alisha Quandt