Day 2 - Breakout 03

Transfer MultiQC Report With scp Exercise (Breakout)

15 Minutes

We just tried two new variations of our MultiQC command, one pointed at the directory of our trimmed FastQC results, and another at the whole project directory. For convenience, we’ve included these reports in the zipped folder you downloaded at the beginning of the class. However, it’s also useful to know how to transfer data to/from a remote instance. We’ll explore how to use scp in this exercise.

Instructions:

• One group member should share their screen in the breakout room. If nobody volunteers, a helper may randomly select someone.
• The group members should discuss the exercise and work together to find a solution.
• After a solution is found, allow time for all members to complete the exercise.

• Make sure that you are viewing your local terminal. The scp command should be run from your own machine.
• Use scp to transfer the trimmed read fastqc report and the comprehensive (all) report from the AWS machine to your personal computer.
• Confirm that you’ve received the reports

Hint: The command format is:

scp source destination

You will need to provide your ssh login information to complete the transfer

Solution - Transfer MultiQC Report With scp Exercise

Helper Hint: On the AWS instance, the multiQC reports have identical filenames. It is helpful to specify the destination filename for each transfer below, so that the reports can be easily differentiated (and don’t overwrite one another).

Helper Hint: Users must know that they should run scp from their local computer, not from the AWS instance.

# Transfer the report of trimmed read results
scp <username>@bfx-workshop01.med.umich.edu:~/RSD_Shell/analysis/out_multiqc_cutadapt/multiqc_report.html ~/rsd-workshop/multiqc_report_trimmed.html
# Transfer the full report
scp <username>@bfx-workshop01.med.umich.edu:~/RSD_Shell/analysis/out_multiqc_all/multiqc_report.html ~/rsd-workshop/multiqc_report_all.html