Exercise 1


Shell command review

Repo shell_practice contains a zipped folder organize_me with files you may have if you run a simulation on a high performance computer. Organize the contents in organize_me using the command line according to the following rules:

  • delete all .input2 files,
  • remove the flags folder and all of its contents,
  • place the test data text files in a folder named test-data,
  • place the .sh files in a folder named shell-scripts,
  • place the .R files in a folder named R-scripts,
  • place the .qsub files in a folder named hpc-run,
  • change the name of folder organize_me to simulation.


# assuming you are in organize_me/
rm *.input2

rm -rf flags/

mkdir test-data/
mv testdata*.txt test-data/

mkdir shell-scripts/
mv *.sh shell-scripts/

mkdir R-scripts/
mv *.R R-scripts/

mkdir hpc-run/
mv *.qsub hpc-run/

cd ../
mv organize_me/ simulation/

Exercise 2


Create a Makefile for the R project in the learn_make repository on GitHub. The target goal should be learn_make.html.

The following steps will guide you in the fileโ€™s development.

  1. Diagram the dependency structure on paper.

  2. First, create a Makefile that only knits the Rmd file and produces the learn_make.html file.

  3. Next, add rules for the data dependencies.

  4. Add phony clean_html and clean_data targets that delete the html file and delete the data, respectively.

  5. Revise your Makefile with built-in variables or other useful features.


.PHONY: all
all: learn_make.html

learn_make.html: learn_make.Rmd data/ok_tor.rds data/fire_stations.rds data/school_districts.rds
    Rscript -e "library(rmarkdown); render('learn_make.Rmd')"

data/ok_tor.rds: R/get_tornadoes.R
    Rscript $<

data/fire_stations.rds: R/get_fire_stations.R
    Rscript $<

data/school_districts.rds: R/get_school_districts.R
    Rscript $<

.PHONY: clean_html clean_data

    rm learn_make.html

    cd data; rm *.rds