GEN220_2025

GEN220 High Throughput Data Analysis

Project maintained by biodataprog Hosted on GitHub Pages — Theme by mattgraham

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).
Create a folder to work in on HPCC (or your own computer): mkdir -p ~/bigdata/gen220/homework and then cd ~/bigdata/gen220/homework
Checkout the GEN220 data folder git clone https://github.com/biodataprog/GEN220_data.git Now you want to make a folder for your work for this class

The steps look like this:

# you can make a folder for GEN220
mkdir gen220
go into that folder
cd gen220
# now use git to checkout the class data folder
git clone https://github.com/biodataprog/GEN220_data.git
# now go into this folder
cd GEN220_data

Look around in the folder. Go into the tabular folder where I’ve stored some tab or comma delimited data. You will later need to copy a file from this folder into your homework folder.

Checkout the homework 1 github repository created in step 2. (if you setup SSH keys in github
```
git clone git@github.com:biodataprog/2025-hw1-YOURGITHUBID
```
OR for the https will need to create a token as your password)
```
git clone https://github.com/biodataprog/2025-hw1-YOURGITHUBID.git
```
Go into your folder (cd 2025-hw1-YOURGITHUBID).
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 achieve the directions at the bottom of this
Test it out (run the ./filecount.sh).
To submit your homework (and you can do this more than once), this requires doing git commit and then git push ```

this step saves a version of the code

git commit -m “This is a homework 1 solution” filesize.sh

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 as script called answer1.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
- count how many kingdom FUNGI are present in the file?
Check in your changes with git commit -m 'a message' and git push to save the changes to github.