UNIX practice

On the UNIX command line. Go into your bigdata folder. If you have not used the cluster before then you will be in the gen220 project. Or you may have your own lab bigdata folder.

See Text Editors in UNIX While it takes a few steps to install and setup, VisualStudio is a great resource you can edit on your local machine but saves changes on HPCC. See https://hpcc.ucr.edu/manuals/hpc_cluster/selected_software/vscode/

This should work

cd ~/bigdata

but if it doesn’t

cd /bigdata/gen220/$USER # will go into your bigdata folder for the class

But if you already had an account on the cluster then

# if the above doesn't work you are likely already in a lab group on HPCC
cd /bigdata/$GROUP/$USER # should work since $USER is your login and $GROUP is your primary lab group
# you can see what groups you are in by typing
groups

For your homework:

Accept the homework 1 problem - (see link in Canvas).
Make a folder for this class and go into it (~/bigdata already points to your class folder /bigdata/gen220/$USER; see UNIX I):
```
mkdir -p ~/bigdata/gen220
cd ~/bigdata/gen220
```

Get the class data (see UNIX II):

git clone https://github.com/biodataprog/GEN220.git        # small example files in GEN220/data
git clone https://github.com/biodataprog/GEN220_data.git   # genomes and tables
ls GEN220_data/tabular

The tabular folder has the comma delimited table you will use below.

Checkout the homework 1 github repository created in step 1 (if you setup SSH keys in github)
```
git clone git@github.com:biodataprog/2026-hw1-YOURGITHUBID.git
```
OR for the https will need to create a token as your password
```
git clone https://github.com/biodataprog/2026-hw1-YOURGITHUBID.git
```
Go into your folder (cd 2026-hw1-YOURGITHUBID). The Git and GitHub guide (Recipe A) walks through these clone/commit/push steps in more detail.
Edit a script in there called filesize.sh; you can do this in jupyter on web, you can edit on the command line with nano, vi, or emacs, or you can use visual studio tunnel
Add some code to this script which achieves the directions at the bottom of this page
Test it out (run the ./filesize.sh).

To submit your homework (and you can do this more than once), this requires doing git commit and then git push

# stage the file (needed the first time you commit a new file, and after every change)
git add filesize.sh
# this step saves a version of the code
git commit -m "This is a homework 1 solution"
# this step will push the data from HPCC or your computer UP to the github site
# this step will request your username (YOURGITHUBID) and your password (that TOKEN I mentioned before).
# if you have setup github account with SSH keys then it will ask you for your SSH key password
git push

You can repeat doing edits to the file, commit, and push to github.

Tasks for Homework 1

copy the threatened-species.csv.gz file - see info here HW1 or you can just run the included ./setup.sh script to download. but also encourage you to practice with cp command.
Write your answers in the script filesize.sh:
- print out the size of the threatened-species.csv.gz using du or ls -l
- Count the number of lines in file
- Print out the number of unique phyla, order_name in the table using cut, sort, uniq (see the UNIX III lab: Data processing with pipes - work through its cut and sort and uniq sections before starting this)
- count how many kingdom FUNGI are present in the file?
Check in your changes with git add, git commit -m 'a message' and git push to save the changes to github. Check the repository page on github.com to make sure your files are there - your last push before the deadline is what gets graded.