A Framework for Bioconductor and R-based Applications on the Cloud

Tutorial on RBioCloud

After successfully installing and configuring RBioCloud, we would recommend that you try out the following simple tutorial for a first hands-on how to use RBioCloud:

Tutorial 1

  1. Step 1:

    Download the sample tutorial here, and extract it to a convenient location. The tutorial1 directory should contain an R script tutorial.R, a Results directory and a RunResults directory. The Results directory stores the results generated by the execution of tutorial1.R on the cloud. The RunResults directory is not submitted onto the cloud, rather stores the results of each run on the host site. Follow similar directory structure for executing any of your jobs.

  2. Step 2:

    Activate the virtual environment where RBioCloud was installed (for example, in ve1 as shown in Installing RBioCloud.)

  3. Step 3:

    Gather resource on the Amazon Cloud using:
    # RBC_GatherResource -rname 'instance1' -rsize 1

  4. Step 4:

    Submit job to Amazon resource using:
    # RBC_SubmitJob -rname 'instance1' -jobdir '/path/tutorial1/'
    /path is the location to the tutorial1 directory.

  5. Step 5:

    Execute job on Amazon resource using:
    # RBC_ExecuteJob -rname 'instance1' -jobdir '/path/tutorial1/' -rscript '/path/tutorial1/tutorial1.R' -runname 'tutorial1_run1'

  6. Step 6:

    Retrieve results from the cloud using:
    # RBC_GetResults -rname 'instance1' -jobdir '/path/tutorial1/' -runname 'tutorial1_run1'
    After you execute the command you can find the results on the host site in the RunResults directory within the tutorial1 directory. A sub-directory with the run name tutorial1_run1 will contain the results.

  7. Step 7:

    Terminate cloud resources using:
    # RBC_TerminateResource -rname 'instance1' -deletevol
    This command releases instance1, deletes the EBS volume attached to instance1 and avoids any further billing on your Amazon account.

The documentation of all RBioCloud commands can be obtained here. Additionally, you can find see the screenshots of the execution of two Bioconductor test cases here.

Thank you for using RBioCloud and for trying out the above tutorial. We hope you find success in your research. Please feel free to contact us , we would be happy to receive your feedback and comments, and assist you wherever possible.