What You Should Know From Lecture: Week 1

Wednesday:

Link to a really cool Shell resource!!!!

We learned to change your Hoffman2 password * Note that this only works in the login nodes * don’t remember what that is? Check the notes from Week 1 Monday

[c177-i0@login3 ~]$ passwd

You will get this prompt

[c177-i0@login3 ~]$ passwd
Changing password for user c177-i0.
Please enter your current password:

You will need to enter your password, but note that you will not be able to see what you typed.
If all goes well you will see the following:

[c177-i0@login3 ~]$ passwd
Changing password for user c177-i0.
Please enter your current password:

Please adhere to the following rules when creating your password:
You cannot use your username or a significant portion of it in your password.
You need to have a minimum of 10 characters.
You need to have at least 5 unique (different) characters.
You need to have at least one character from 3 different character classes.
The character classes are: UPPERCASE CHARACTERS, lowercase characters, digits (0-9),
    and punctuation ((  !#%&)(+*-,/.;=<?>@[]\_^`{}|~  )).
Please enter your NEW password:

I recommend making your password a sassy sentance but that is just me….
If Hoffman2 accepts your new password it will ask you this:

Please re-enter your new password:

Password saved.  Strength: very strong.
Please allow up to 15 minutes for your password to propagate to all cluster nodes.
[c177-i0@login3 ~]$

If you type the same password twice, it will be accepted.

Tip to make your life easier: use tab to complete your path

Lets make and delete stuff!

to make a new directory use mkdir

[c177-i0@n2010 ~]$ mkdir example_dir

I will now have a directory named example_dir

[c177-i0@n2010 ~]$ ls
classdata  eeb-177  example_dir  scratch

if I include a blank space in my directory name bad stuff happens…

[c177-i0@n2010 ~]$ mkdir example dir
[c177-i0@n2010 ~]$ ls
classdata  dir  eeb-177  example  example_dir  scratch

I made two directories ‘example’ and ‘dir’
I can also make multiple directories in the same go using the flag -p
It makes the parent directories for any nested directories
I wanted to make and ‘example_1’ directory that contains and ‘example_A’ directory in the directory ‘example’

[c177-i0@n2010 ~]$ mkdir -p example/example_1/example_A

I can then cd into example_A and check that I have the path that I expect

[c177-i0@n2010 ~]$ cd example/example_1/example_A
[c177-i0@n2010 example_A]$ pwd
/u/home/class/c177/c177-i0/example/example_1/example_A

Let learn to remove the mistakenly made directories ‘example’ and ‘dir’, but remember once it is gone it is really gone so be careful.

there are several ways to remove a directory
try using rmdir

[c177-i0@n2010 ~]$ rmdir example
[c177-i0@n2010 ~]$ ls
classdata  dir  eeb-177  example_dir  scratch

you can also use rm -r
the -r stands for recursive (deletes everything in the directory)

[c177-i0@n2010 ~]$ rm -r dir
[c177-i0@n2010 ~]$ ls
classdata  eeb-177  example_dir  scratch

if you try this without the -r you will get the following

[c177-i0@n2010 ~]$ rm dir
rm: cannot remove `dir': Is a directory

Now lets make a file in example_dir

we can cd into the directory, then make the file using the command ‘touch’

[c177-i0@n2010 ~]$ cd example_dir/
[c177-i0@n2010 example_dir]$ touch example.txt
[c177-i0@n2010 example_dir]$ ls
example.txt

now we have an empty text file with the following path: /u/home/class/c177/c177-i0/example_dir/example.txt
I figured this out by using the command pwd
I can also make this file from my home directory by doing the following

[c177-i0@n2010 ~]$ touch /u/home/class/c177/c177-i0/example_dir/example.txt

I can use ‘ls -R’ to see that the file ‘example.txt’ is contained in the new example dir directory

[c177-i0@n2010 ~]$ ls -R
.:
classdata  eeb-177  example  example_dir  scratch

./eeb-177:
Favorite_animal.txt  README.txt  W1-Discussion-In-class.txt

./example:
example_1

./example/example_1:
example_A

./example/example_1/example_A:

./example_dir:
example.txt

it also shows me the contents of the eeb-177 directory made for the discussion exercise and the two directories that we made in directory example
I am now going to remove the ‘example.txt’ file that I made using rm
I can cd into example_dir and then delete it

[c177-i0@n2010 ~]$ cd example_dir/
[c177-i0@n2010 example_dir]$ ls
example.txt
[c177-i0@n2010 example_dir]$ rm example.txt
[c177-i0@n2010 example_dir]$ ls

I can also remove it from my home directory if I know the path to the file

[c177-i0@n2010 ~]$ rm example_dir/example.txt
[c177-i0@n2010 ~]$ ls
classdata  eeb-177  example  example_dir  scratch
[c177-i0@n2010 ~]$ ls example_dir/
[c177-i0@n2010 ~]$

If I want to be a little safer about using rm I can use the flag -*

[c177-i0@n2010 example_dir]$ ls
example.txt
[c177-i0@n2010 example_dir]$ rm -i example.txt
rm: remove regular empty file `example.txt'? y
[c177-i0@n2010 example_dir]$ ls
[c177-i0@n2010 example_dir]$

if it was a mistake to type rm I can say no

[c177-i0@n2010 example_dir]$ rm -i example.txt
rm: remove regular empty file `example.txt'? n
[c177-i0@n2010 example_dir]$ ls
example.txt

Lets look at a file

cd into ‘~/classdata/Week1/Wednesday_in_class’
notice that I am using the ~ for the home directory
this directory contains the following:

[c177-i0@n2010 Wednesday_in_class]$ ls
README.populations               sort_ex_2.txt    uniq_color3.txt
README.populations.modified.txt  uniq_color1.txt  uniq_ex_1.txt
sort_ex_1.txt                    uniq_color2.txt

I can look at the entire contents of these files using ‘less’

[c177-i0@n2010 Wednesday_in_class]$ less sort_ex_1.txt

the Shell will show me something that looks like this

Griffon Bleu de Gascogne
Segugio Italiano
Blue Heeler
Pachon Navarro
Treeing Tennessee Brindle
Ratonero Valenciano
Maltese
Labradoodle
Bruno Jura Hound
Cesky Fousek
Armant
Stabyhoun
sort_ex_1.txt (END)

to get back to the command prompt use ‘q’
I can also look at the top ten lines of the file using ‘head’. 10 lines is the default

[c177-i0@n2010 Wednesday_in_class]$ head sort_ex_1.txt
Griffon Bleu de Gascogne
Segugio Italiano
Blue Heeler
Pachon Navarro
Treeing Tennessee Brindle
Ratonero Valenciano
Maltese
Labradoodle
Bruno Jura Hound
Cesky Fousek
[c177-i0@n2010 Wednesday_in_class]$

I can look at any number of lines using the flag -n

[c177-i0@n2010 Wednesday_in_class]$ head -n 3 sort_ex_1.txt
Griffon Bleu de Gascogne
Segugio Italiano
Blue Heeler
[c177-i0@n2010 Wednesday_in_class]$

-n 3 printed only the first three lines
‘tail’ will show me the bottom ten lines (by default)

[c177-i0@n2010 Wednesday_in_class]$ tail sort_ex_1.txt
Blue Heeler
Pachon Navarro
Treeing Tennessee Brindle
Ratonero Valenciano
Maltese
Labradoodle
Bruno Jura Hound
Cesky Fousek
Armant
Stabyhoun[c177-i0@n2010 Wednesday_in_class]$

I can also use the -n flag with tail

[c177-i0@n2010 Wednesday_in_class]$ tail -n 2 sort_ex_1.txt
Armant
Stabyhoun[c177-i0@n2010 Wednesday_in_class]$

Note that the command prompt is on the same line as the last line of the file. This is because I did not add a new line to the end of my file.

Lets build a directory

In ‘~/classdata/Week1/Monday_in_class’ there is a file called ‘Do_first_Build_directory_exercise.txt’
this file contains

[c177-i0@n2010 Monday_in_class]$ head ~/classdata/Week1/Monday_in_class/Do_first_Build_directory_exercise.txt
lecture_1
└── syllabus
    ├── full_document
    └── partial_document


[c177-i0@n2010 Monday_in_class]$

Build this directory structure from your home directory
There are many ways to do this.
here is one example

[c177-i0@n2010 Monday_in_class]$ mkdir -p $HOME/Lecture_1/syllabus/full_document
[c177-i0@n2010 Monday_in_class]$ mkdir -p $HOME/Lecture_1/syllabus/partial_document

I can check it is in home using ‘ls -R’

[c177-i0@n2010 Monday_in_class]$ ls -R $HOME
/u/home/class/c177/c177-i0:
classdata  eeb-177  example  example_dir  Lecture_1  scratch

/u/home/class/c177/c177-i0/eeb-177:
Favorite_animal.txt  README.txt  W1-Discussion-In-class.txt

/u/home/class/c177/c177-i0/example:
example_1

/u/home/class/c177/c177-i0/example/example_1:
example_A

/u/home/class/c177/c177-i0/example/example_1/example_A:

/u/home/class/c177/c177-i0/example_dir:
example.txt

/u/home/class/c177/c177-i0/Lecture_1:
syllabus

/u/home/class/c177/c177-i0/Lecture_1/syllabus:
full_document  partial_document

/u/home/class/c177/c177-i0/Lecture_1/syllabus/full_document:

/u/home/class/c177/c177-i0/Lecture_1/syllabus/partial_document:
[c177-i0@n2010 Monday_in_class]$

I could have also done this

[c177-i0@n2010 Monday_in_class]$ cd ~
[c177-i0@n2010 ~]$ mkdir Lecture_1
[c177-i0@n2010 ~]$ cd Lecture_1/
[c177-i0@n2010 Lecture_1]$ mkdir full_document
[c177-i0@n2010 Lecture_1]$ mkdir partial_document

I can think of several other ways to accomplish this task
Can you make a file structure from Lecture_1 that looks like this and contains a file?

lecture_1
└── folders_for_file
    └── folder_A
          |── folder_A.1
          |── folder_A.2 -- file_for_folder_A.2.txt
          └── folder_A.3

Copying files between directories

Use the command ‘cp’. It works like this
cp
lets move the file syllabus.txt from the directory ~/classdata/Week1/Monday_in_class and move it to the directory ~/Lecture_1/syllabus/full_document

[c177-i0@n2010 ~]$ cp ~/classdata/Week1/Monday_in_class/syllabus.txt ~/Lecture_1/syllabus/full_document/
[c177-i0@n2010 ~]$ ls ~/Lecture_1/syllabus/full_document/
syllabus.txt
[c177-i0@n2010 ~]$

now I can look at the contents of the file

[c177-i0@n2010 ~]$ head ~/Lecture_1/syllabus/full_document/syllabus.txt
# __Practical Computing for Evolutionary Biologists and Ecologists Syllabus; EEB C177/C234__
Course Basic Information |  Course Logistics  
--- | ---
__Spring 2019__ <br> __Letter grading__ <br>  __Units:__ 4 <br> __Prerequisite:__ Life Sciences 1 or 7B. | __Lecture:__ MW 8-9:15; Physics and Astronomy Building Room 2748 <br>  __Computer Lab:__ T or R 1-2:50; WGYoung 4067 <br> __Course Website:__ <br> __Github classroom:__ <br> https://classroom.github.com/classrooms/47793618-pceeb-practical_computing_sp2019

____
## Instructor: Emily Curd <br>
eecurd@g.ucla.edu<br>
__Office Hours:__ MW 9:30-10:30 Music School Café
<br> The best way to contact me is by email or through the course GitHub.
[c177-i0@n2010 ~]$

What You Should Know From Lecture: Week 1

Wednesday:

Link to a really cool Shell resource!!!!

Tip to make your life easier: use tab to complete your path

Wednesday Challenge