diff --git a/docs/Intro_to_Unix/Intro_to_Unix_Part_1.html b/docs/Intro_to_Unix/Intro_to_Unix_Part_1.html index 4f43156..fbd0ae9 100644 --- a/docs/Intro_to_Unix/Intro_to_Unix_Part_1.html +++ b/docs/Intro_to_Unix/Intro_to_Unix_Part_1.html @@ -324,6 +324,9 @@

Shell commands are basic instructions used to perform specific tasks.

command_name -[option(s)] [argument(s)]

Example:

+
+
ls -lah part_1
+

Here we are providing multiple options to the ls command and the directory part_1 as an argument

+
message="Hello, World"
+echo $message
Hello, World
@@ -613,6 +621,9 @@ macOS 14.4 January 9, 2021 macOS 14.4
  • You can also cycle through previously run commands using the up and down arrow keys
  • By default bash stores the last 500 commands, zsh stores the last 1000
    • +
    +
    history
    +
    @@ -660,7 +671,7 @@ What is the realative path to file1.txt if the working director

    pwd: print working directory

    -
    pwd
    +
    pwd
    @@ -674,7 +685,7 @@ What is the realative path to file1.txt if the working director

    ls: list contents of a directory

    -
    ls .
    +
    ls .
    part_1
 part_2
@@ -687,11 +698,11 @@ unix_workshop.tar.gz
  • -h file sizes in human readable format (e.g., 1K, 2G)
    • -
    ls -lah part_1
    +
    ls -lah part_1
    total 8
-drwx---r--@ 4 nelphick  staff   128B Nov 11 10:58 .
-drwxr-xr-x@ 6 nelphick  staff   192B Nov 11 10:58 ..
+drwx---r--@ 4 nelphick  staff   128B Nov 11 11:00 .
+drwxr-xr-x@ 6 nelphick  staff   192B Nov 11 11:00 ..
 -rw-r--r--@ 1 nelphick  staff     0B Apr 11  2023 .hidden_file.txt
 -rw-r--r--@ 1 nelphick  staff    60B Apr 12  2023 list_numbers.tsv
    @@ -700,8 +711,8 @@ drwxr-xr-x@ 6 nelphick staff 192B Nov 11 10:58 ..

    cd: move to a directory

    -
    cd unix_workshop/part_1
-ls -l
    +
    cd unix_workshop/part_1
+ls -l
    @@ -710,14 +721,14 @@ drwxr-xr-x@ 6 nelphick staff 192B Nov 11 10:58 ..
    -
    cd ..
-ls -l
    +
    cd ..
+ls -l
    total 8
-drwx---r--@ 4 nelphick  staff   128 Nov 11 10:58 part_1
-drwxr-xr-x@ 3 nelphick  staff    96 Nov 11 10:58 part_2
+drwx---r--@ 4 nelphick  staff   128 Nov 11 11:00 part_1
+drwxr-xr-x@ 3 nelphick  staff    96 Nov 11 11:00 part_2
 -rw-r--r--  1 nelphick  staff  1790 Nov 11 10:43 unix_workshop.tar.gz
    @@ -755,7 +766,7 @@ drwxr-xr-x@ 3 nelphick staff 96 Nov 11 10:58 part_2

    touch: create an empty file

    -
    touch new_file.txt
    +
    touch new_file.txt
    • If the file exists, it will update the time stamp
      • @@ -764,7 +775,7 @@ drwxr-xr-x@ 3 nelphick staff 96 Nov 11 10:58 part_2

      mkdir: make a directory

      -
      mkdir new_directory
      +
      mkdir new_directory
      • -p make parent directories if they don’t exist
        • @@ -773,19 +784,19 @@ drwxr-xr-x@ 3 nelphick staff 96 Nov 11 10:58 part_2

        mv: move a file or folder

        -
        mv new_file.txt new_directory
        +
        mv new_file.txt new_directory
        • Also used to rename files/folders
        -
        mv new_directory/new_file.txt new_directory/new_file1.txt
        +
        mv new_directory/new_file.txt new_directory/new_file1.txt

        cp: copy a file or folder

        -
        cp new_directory/new_file1.txt new_directory/new_file2.txt
        +
        cp new_directory/new_file1.txt new_directory/new_file2.txt
        • -r to copy a folder (recursive)
          • @@ -797,13 +808,13 @@ drwxr-xr-x@ 3 nelphick staff 96 Nov 11 10:58 part_2
        • This command should always be used with care since the files it is used on cannot be recovered
        -
        rm new_directory/new_file2.txt
        +
        rm new_directory/new_file2.txt

        du: check the size of a file or folder

        -
        du -h */*
        +
        du -h */*
          0B    new_directory/new_file1.txt
 4.0K    part_1/list_numbers.tsv
        @@ -827,7 +838,7 @@ drwxr-xr-x@ 3 nelphick staff 96 Nov 11 10:58 part_2

        nano

        -
        nano new_directory/new_file1.txt
        +
        nano new_directory/new_file1.txt
        @@ -876,7 +887,7 @@ drwxr-xr-x@ 3 nelphick staff 96 Nov 11 10:58 part_2
      • curl supports multiple protocols but the most commonly used one is HTTPS
      -
      curl -o part_2/homo_sapiens.refseq.tsv.gz https://ftp.ensembl.org/pub/current_tsv/homo_sapiens/Homo_sapiens.GRCh38.115.refseq.tsv.gz
      +
      curl -o part_2/homo_sapiens.refseq.tsv.gz https://ftp.ensembl.org/pub/current_tsv/homo_sapiens/Homo_sapiens.GRCh38.115.refseq.tsv.gz
      • -o gives the output file name and location
        • @@ -892,7 +903,7 @@ drwxr-xr-x@ 3 nelphick staff 96 Nov 11 10:58 part_2
    -
    scp /path/to/local/file user@remote.host:/path/to/remote/directory
    +
    scp /path/to/local/file user@remote.host:/path/to/remote/directory
    @@ -907,7 +918,7 @@ drwxr-xr-x@ 3 nelphick staff 96 Nov 11 10:58 part_2

  • Regular Expressions : sequence of characters that forms a search pattern

    • -
    grep "7" part_1/list_numbers.tsv
    +
    grep "7" part_1/list_numbers.tsv
    7   8   52  13  6   42  79  1
 13  4   9   82  67  71  93  3
    @@ -935,7 +946,7 @@ drwxr-xr-x@ 3 nelphick staff 96 Nov 11 10:58 part_2
    -
    grep "3$" part_1/list_numbers.tsv
    +
    grep "3$" part_1/list_numbers.tsv
    1   3   6   10  11  22  0   3
 13  4   9   82  67  71  93  3
    @@ -945,13 +956,13 @@ drwxr-xr-x@ 3 nelphick staff 96 Nov 11 10:58 part_2

    head/tail: view the first or last n lines of a file

    -
    head -n 1 part_1/list_numbers.tsv
    +
    head -n 1 part_1/list_numbers.tsv
    1   3   6   10  11  22  0   3
    -
    tail -n 1 part_1/list_numbers.tsv
    +
    tail -n 1 part_1/list_numbers.tsv
    13  4   9   82  67  71  93  3
    @@ -964,7 +975,7 @@ drwxr-xr-x@ 3 nelphick staff 96 Nov 11 10:58 part_2

    cat: print the contents of a file

    -
    cat part_1/list_numbers.tsv
    +
    cat part_1/list_numbers.tsv
    1   3   6   10  11  22  0   3
 7   8   52  13  6   42  79  1
@@ -975,7 +986,7 @@ drwxr-xr-x@ 3 nelphick  staff    96 Nov 11 10:58 part_2
 
    
 
    cut: get specific columns from a file
    
 
    
-
    cut -f 1-3,6 part_1/list_numbers.tsv
    
+
    cut -f 1-3,6 part_1/list_numbers.tsv
    
 
    
 
    1   3   6   22
 7   8   52  42
@@ -996,7 +1007,7 @@ drwxr-xr-x@ 3 nelphick  staff    96 Nov 11 10:58 part_2
 
  • Chaining commands allows you to do complex operations on text streams
    • 
 
 
    
-
    grep "3$" part_1/list_numbers.tsv | cut -f 1-3
    
+
    grep "3$" part_1/list_numbers.tsv | cut -f 1-3
    
 
    
 
    1   3   6
 13  4   9
    
@@ -1009,14 +1020,14 @@ drwxr-xr-x@ 3 nelphick  staff    96 Nov 11 10:58 part_2
 
  • The output of any command can be written to a file with the ” > ” character
    • 
 
 
    
-
    grep "3$" part_1/list_numbers.tsv | cut -f 1-3 > part_1/subset_list_numbers.tsv
    
+
    grep "3$" part_1/list_numbers.tsv | cut -f 1-3 > part_1/subset_list_numbers.tsv
    
 
    
 
    
 
    
 
    tr: translate or substitute characters
    
 
    
-
    cat part_1/list_numbers.tsv | tr "\t" "," > part_1/list_numbers.csv
-cat part_1/list_numbers.csv
    
+
    cat part_1/list_numbers.tsv | tr "\t" "," > part_1/list_numbers.csv
+cat part_1/list_numbers.csv
    
 
    
 
    1,3,6,10,11,22,0,3
 7,8,52,13,6,42,79,1
@@ -1027,7 +1038,7 @@ drwxr-xr-x@ 3 nelphick  staff    96 Nov 11 10:58 part_2
 
    
 
    sort: sort values
    
 
    
-
    cat part_1/list_numbers.csv | cut -d "," -f 1 | sort -n
    
+
    cat part_1/list_numbers.csv | cut -d "," -f 1 | sort -n
    
 
    
 
    1
 7
@@ -1038,7 +1049,7 @@ drwxr-xr-x@ 3 nelphick  staff    96 Nov 11 10:58 part_2
 
  • -n : sort numerically (default is alphabetical)
    • 
 
 
    
-
    cat part_1/list_numbers.csv | cut -d "," -f 8 | sort -nu
    
+
    cat part_1/list_numbers.csv | cut -d "," -f 8 | sort -nu
    
 
    
 
    1
 3
    
diff --git a/docs/Intro_to_Unix/Intro_to_Unix_Part_2.html b/docs/Intro_to_Unix/Intro_to_Unix_Part_2.html
index 75232ff..3ad1266 100644
--- a/docs/Intro_to_Unix/Intro_to_Unix_Part_2.html
+++ b/docs/Intro_to_Unix/Intro_to_Unix_Part_2.html
@@ -306,9 +306,9 @@
 ls -l
    
 
    
 
    total 16
-drwx---r--@ 4 nelphick  staff   128 Nov 11 11:00 part_1
--rw-r--r--  1 nelphick  staff   800 Nov 11 11:00 part_1.tar.gz
-drwxr-xr-x@ 4 nelphick  staff   128 Nov 11 11:00 part_2
+drwx---r--@ 4 nelphick  staff   128 Nov 11 12:31 part_1
+-rw-r--r--  1 nelphick  staff   800 Nov 11 12:32 part_1.tar.gz
+drwxr-xr-x@ 4 nelphick  staff   128 Nov 11 12:32 part_2
 -rw-r--r--  1 nelphick  staff  1790 Nov 11 10:43 unix_workshop.tar.gz
    
 
    
 
    
@@ -473,7 +473,7 @@ ENSG00000149527 ENST00000449969 ENSP00000397289 XM_047435038    RefSeq_mRNA_pred
 
    
 
    ls -l part_2/example_script.sh
    
 
    
-
    -rw-r--r--  1 nelphick  staff  287 Nov 11 11:00 part_2/example_script.sh
    
+
    -rw-r--r--  1 nelphick  staff  287 Nov 11 12:32 part_2/example_script.sh
    
 
    
 
    
 
      
@@ -483,7 +483,7 @@ ENSG00000149527 ENST00000449969 ENSP00000397289 XM_047435038    RefSeq_mRNA_pred
 
      chmod u+x part_2/example_script.sh
 ls -l part_2/example_script.sh
      
 
      
-
      -rwxr--r--  1 nelphick  staff  287 Nov 11 11:00 part_2/example_script.sh
      
+
      -rwxr--r--  1 nelphick  staff  287 Nov 11 12:32 part_2/example_script.sh
      
 
      
 
    
 
    
diff --git a/intro-unix-command-line/Intro_to_Unix_Part_1.qmd b/intro-unix-command-line/Intro_to_Unix_Part_1.qmd
index cc31976..fa39332 100644
--- a/intro-unix-command-line/Intro_to_Unix_Part_1.qmd
+++ b/intro-unix-command-line/Intro_to_Unix_Part_1.qmd
@@ -142,6 +142,7 @@ Shell commands are basic instructions used to perform specific tasks.
 Example:
 ```{bash}
 #| eval: false
+#| echo: true
 ls -lah part_1
 ```
 
@@ -151,6 +152,11 @@ Here we are providing multiple options to the `ls` command and the directory **p
 
 ## man: pull up the manual page for a command
 
+```{bash}
+#| echo: true
+#| eval: false
+man echo
+```
 
 
 ```{bash}
@@ -172,6 +178,7 @@ man -P cat man | col -b
 - **Variables** : a named container that holds a value or data
 - **Strings** : sequence of characters
 ```{bash}
+#| echo: true
 message="Hello, World"
 echo $message
 ```
@@ -183,6 +190,8 @@ Here, we assign the string "Hello, World!" to the variable `message` and use ech
 - By default bash stores the last 500 commands, zsh stores the last 1000
 
 ```{bash}
+#| echo: true
+#| eval: false
 history
 ```