Refresher for Unix 101, part 2

Last updated on 2024-11-19 | Edit this page

Overview

Questions

  • What are the basic Unix commands we covered in Unix 101, part 1?

Objectives

  • Review Unix 101, part 1 material

Open the collaborative doc for our workshop http://broad.io/cb-unix-20241031

If you haven’t already, please complete your workshop setup https://broad.io/cb-unix-setup

Feel free to browse today’s lesson content

Unix review

Log onto the Broad login server

If you are on-site, connect to the Broad-Internal wireless network. If you are off-site, connect to the Broad VPN.

Download cb_unix_shell.tgz to your home directory and unpack it.

BASH 

$ cd
$ wget https://github.com/jlchang/cb-unix-shell-lesson-template/raw/main/learners/files/cb_unix_shell.tgz
$ tar -xzf cb_unix_shell.tgz

In Unix 101, part 1 we learned how to use pwd to find our current location within our file system. We also learned how to use cd to change locations and ls to list the contents of a directory.

Let’s use these commands to navigate to the cb_unix_shell directory. First, change directory to your home directory and list the contents in the directory, just to make sure we know where we are.

BASH 

$ cd
$ ls

See the tilde (~) in your Unix prompt? This indicates you’re in your Unix home directory.

OUTPUT 

cb_unix_shell/  cb_unix_shell.tar

Now change to a subdirectory within your home directory.

BASH 

$ cd cb_unix_shell

Notice that where the tilde was in your Unix prompt, you now see ~/cb_unix_shell. Your Broad Unix prompt is set up to show you your current working directory. Right now you’re in the cb_unix_shell directory within your Unix home directory.

Let’s look at the content in the cb_unix_shell subdirectory.

BASH 

$ ls

OUTPUT 

Dahl/  Seuss/  authors.txt  data  prodinfo454/

Let’s have a look around. First, print your current working directory.

BASH 

$ pwd

pwd will return show you the full path from the root directory to your current working directory

OUTPUT 

/home/unix/jlchang/cb_unix_shell

List the directory contents using the long format

BASH 

$ ls -l

OUTPUT 

total 515
drwxr-sr-x   4 jlchang sequence    94 May  8 01:53 Dahl/
drwxr-sr-x   4 jlchang sequence    68 May  8 01:56 Seuss/
-rw-r--r--   1 jlchang sequence   155 Mar 14  2013 authors.txt
-rw-r--r--   1 jlchang sequence 19085 Mar 14  2013 data
drwxr-sr-x 268 jlchang sequence 19483 May  8 01:55 prodinfo454/

Use the relative path (..) to go “up” a directory

BASH 

$ cd ..

Notice the path in your Unix prompt is back to tilde (~)

Let’s navigate to the Dahl/James_and_the_Giant_Peach/ directory using tab completion for efficiency and less typing

BASH 

$ cd c<tab>/D<tab>/J<tab>

Thanks to tab completion, your command line should look like cd cb_unix_shell/Dahl/James_and_the_Giant_Peach/

Use the tilde (~) special character to help navigate directly to the cb_unix_shell/prodinfo454 directory in your home directory.

BASH 

$ cd ~/c<tab>/p<tab>

Your tab completed command line should look like cd ~/cb_unix_shell/prodinfo454/

Wildcards

prodinfo454 is the directory where we had a ton of stuff. You can get a list of everything with ls BUT you can also be selective by using a wildcard. * matches zero or more characters. Using *, you can list only run folders from the snap machine.

BASH 

$ ls -d *snap*

OUTPUT 

R_2009_01_16_11_50_39_snap_levesque_TresFusoUnoColiRUN647204/
R_2009_01_30_12_11_52_snap_jdiaz_HMProchloroRUN702823/
R_2009_06_19_11_34_42_snap_aholling_0619TFSnapRun646641/
R_2009_07_09_11_24_35_snap_krizzolo_krizzolo070909RUN715150/
R_2009_07_15_11_57_04_snap_krizzolo_15julydosjdcRun713445/
R_2009_07_31_10_57_24_snap_jdiaz_31julyjdcRun718215/
R_2009_09_14_16_33_10_snap_aholling_HossBDayRun718349/
R_2009_09_16_14_13_24_snap_krizzolo_091609KRRun718211/
R_2009_10_02_11_21_01_snap_krizzolo_100209Run718213/
R_2009_11_12_13_13_37_snap_krizzolo_111209_16s2_KRRun715342/

The ? wildcard matches exactly one character. Can you see how using the ? wildcard in this command line limits the listed run folders to crinkle runs from February or December 2009?

BASH 

$ ls -d R_2009_?2_*crinkle*

OUTPUT 

R_2009_02_18_13_14_30_crinkle_pfrere_TICycleReduxRUN705472/
R_2009_12_04_11_12_45_crinkle_krizzolo_elgranvaronblastoRun720551/
R_2009_12_08_13_19_52_crinkle_krizzolo_8regionKRRun720565/
R_2009_12_14_11_22_09_crinkle_krizzolo_2regionKRRun722286/

Now that we’ve reviewed how to move around, let’s play with some files! Let’s look in one of these directories and see what’s in them. (Note: run folders hold a lot of information, we’ve removed the majority of the data, leaving only the aaLog.txt files.)

BASH 

$ ls -d *Tues*

OUTPUT 

R_2010_07_27_11_06_59_pop_jdiaz_dmTuesrun738071/

BASH 

$ cd *Tues*             # if your wildcard matches more than one, cd will take the first

Your command prompt should show ~/cb_unix_shell/prodinfo454/R_2010_07_27_11_06_59_pop_jdiaz_dmTuesrun738071 as the path for your current working directory.

Examining Files

BASH 

$ cat aaLog.txt         # output not shown below - too long!
$ head !$               # use your history (!) and grab the last word ($) from the previous command

Variable substitution will result in this command line head aaLog.txt

OUTPUT 

nPixelsUnderDCOffset = 11849 (0.070626 %)
adjusting dc offset
found 4 regions
region 0: center = 520, width = 794
region 1: center = 1544, width = 788
region 2: center = 2584, width = 792
region 3: center = 3598, width = 782
range 0: start = 259, end = 781
range 1: start = 1283, end = 1805
range 2: start = 2323, end = 2845

tail will show the last 10 lines

BASH 

$ tail aaLog.txt

OUTPUT 

newApyraseWashPulseWidth = 202.298
adjusted pulse width is 202
changing micro's pulse width to 202
process image block...
apyrase adjust done
MsgType = 108, Index = 27, Pulse = 202
SCRIPT_PULSE_WIDTH_NOTIFY msg received
MsgType = 204, Index = 27, Pulse = 202
Run Complete Msg received
run log ends

You can use a paging file viewer to control your view of the file content. Remember, to proceed, q to quit.

BASH 

$ less aaLog.txt

Creating, moving, copying, and removing

Make a copy of a file, in your current working directory, your home directory,

BASH 

$ cp aaLog.txt copy.txt
$ ls                           # see the copy you created

OUTPUT 

aaLog.txt  copy.txt

Let’s remind ourselves, what’s in your home directory?

BASH 

$ ls ~

OUTPUT 

cb_unix_shell/  cb_unix_shell.tar

Make a copy of aaLog.txt in your home directory, using the special character tilde (~).

BASH 

$ cp aaLog.txt ~/copy2.txt     
$ ls                           # Now what's in your current directory *Use up arrow 3x*

OUTPUT 

aaLog.txt  copy.txt

Compre with what’s in your home directory - is it what you expected?

BASH 

$ ls ~

OUTPUT 

cb_unix_shell/	cb_unix_shell.tar  copy2.txt

Moving and renaming files

These commands look similar to cp but be careful, the differences are important.

BASH 

$ mv aaLog.txt copy3.txt       # if the second argument for "mv" isn't a directory, you're renaming
$ ls

Notice aaLog.txt is gone, you renamed it!

OUTPUT 

copy.txt  copy3.txt

Check what’s in your home directory.

BASH 

$ ls  ~

OUTPUT 

cb_unix_shell/	cb_unix_shell.tar  copy2.txt

Move aaLog.txt to your home directory, using the special character tilde (~).

BASH 

$ mv copy.txt ~                # tilde (~) shortcut for your home directory => moving, not renaming
$ ls

OUTPUT 

copy3.txt

BASH 

$ ls ~                         # what's in your home directory now? *Use up arrow 3x*

OUTPUT 

cb_unix_shell/	cb_unix_shell.tar  copy.txt  copy2.txt

Rename one of the copies to restore aaLog.txt

BASH 

$ mv copy3.txt aaLog.txt        # aaLog.txt is not a directory => renaming, not moving
$ ls                           # what's in your current directory now? *Use up arrow 3x*

OUTPUT 

aaLog.txt

Create a directory

BASH 

$ mkdir test
$ ls

OUTPUT 

test

Copy a file into the test directory

BASH 

$ cp aaLog.txt test 
$ ls

OUTPUT 

aaLog.txt  test/

What’s in the test directory?

BASH 

$ ls test                     

```output
aaLog.txt

List what’s in your current directory, recursively

BASH 

$ ls -R                        #

OUTPUT 

.:
aaLog.txt  test/

./test:
aaLog.txt

BASH 

$ rmdir test                   # try to remove the test directory

You’ll see this error because rmdir can only run on empty directories

OUTPUT 

rmdir: failed to remove 'test': Directory not empty

BASH 

$ rm -rf test                  # force remove the test directory, recursively (include contents)
$ ls

OUTPUT 

aaLog.txt

Key Points

  • We’ve reviewed navigation, file content viewing, file manipulation.
  • We’re ready to learn about how you can use these Unix command line techniques and deploy them to perform tasks in a repeatable, effort-saving manner!