Morning Setup and Final Checklist

Did you?

  1. Email your TA the k4.png file after conda install 5 programs
  2. Email your TA an IGV screenshot for HUES64_rep1.mRNA.chr20.bw
  3. Check your 12 R packages are installed e.g. library( "annotatr" )

Do each morning by 9:00am …

  1. Help – Monitor #questions from your Slack.app (laptop and phone)

  2. Unix – Load programs installed via conda on MARCC

    ssh gateway2.marcc.jhu.edu -l username@jhu.edu
srun -p shared -c 1 --mem 1024 -t 120 --pty bash
module load anaconda-python/3.6
source activate pg2018
deeptools
  3. Transfer – Practice copying a file from MARCC

    • Scroll to see entire command … ends in Desktop/PG2018/...

      scp username@jhu.edu@gateway2.marcc.jhu.edu:work/test.txt Desktop/PG2018/monday.txt
    • Check that file exists on your laptop by opening it
  4. IGV – Start genomic visualization tool
    • Test by loading HUES64_rep1.mRNA.chr20.bw and zooming into DNMT3B gene
  5. RStudio – Start integrated development environment for R
    • Test by library( "annotatr" )
  6. Notes – Store commands using TextEdit.app or Wordpad
    • Be sure to disable auto-correct features
      • e.g. Uncheck in TextEdit > Preferences
        • Correct spelling automatically
        • Smart quotes
        • Smart dashes