999_appendices.Rmd

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

# **Appendices**

## **Other workshop files**

[First workshop material](http://hpcworkshop.vai.org)

## **Local access of files on the HPC**

Mac: 
1. Click Finder > "Go" in task bar > "Connect to Server" in the pulldown menu.
2. Type `smb://pn.vai.org` and click "Connect".
3. Select 'projects' and 'researchtemp'. Click "OK".
4. You can now navigate using Finder, or type `ls /Volumes/projects/` or `ls /Volumes/researchtemp/` in the Terminal.

Windows:
* In File Explorer, type `\\pn.vai.org\` and hit Enter.

## **Bash cheatsheet**

```{r bash_cheatsheet, results='asis', echo=FALSE}
library(kableExtra)
library(knitr)

commands <- data.frame(
  Name = c(
    "Print Working Directory",
    "List",
    "List More Detail",
    "Make Directory",
    "Move",
    "Change Directory",
    "Remove",
    "Copy",
    "Search for File",
    "Head",
    "Tail",
    "Less",
    "More",
    "Quit",
    "Concatenate",
    "Search for Text",
    "Word, Line, and Character Count",
    "Touch"),

  Command_Line = c(
    "`pwd`",
    "`ls`",
    "`ls -lht`",
    "`mkdir`",
    "`mv`",
    "`cd`",
    "`rm`",
    "`cp`",
    "`find`",
    "`head`",
    "`tail`",
    "`less`",
    "`more`",
    "`q`",
    "`cat`",
    "`grep`",
    "`wc`",
    "`touch`"),

  Description = c(
    "Displays the current working directory",
    "Lists the files and directories in the current directory",
    "Display more details about the file",
    "Creates a new directory",
    "Moves or renames files or directories",
    "Change to an existing directory",
    "Deletes files and directories",
    "Copies files or directories",
    "Search for files and directories based on various criteria like name, size, and modification time",
    "Display at the beginning of a file",
    "Display at the end of a file",
    "Load the necessary portion of a file",
    "Load the entire file",
    "Stop viewing the current file",
    "Display the contents of a file",
    "Search for a specific pattern of text within files",
    "Display the number of words, lines, and characters in a file",
    "Create a new empty file"),

 Example = c(
  # explanation_1
  "**`[username\\@submit002 ~]$ pwd`**\n\nResult:/home/username",


  # explanation_2

  "**`[username\\@submit002 ~]$ ls`**\n\nResult: It returns empty after the $
  symbol since nothing has been created.",

 " **`[username\\@submit002 ~]$ ls -lht`**\n\nResult: Display file detail in the current director",

  # explanation_3
  "**`[username\\@submit002 ~]$ mkdir hpc_mini_workshop`**\n\nResult: A hpc_mini_workshop folder is created.",

  # explanation_4
  "**`[username\\@submit002 ~]$ mv hpc_mini_workshop workshopTraining`**\n\nResult: Now the hpc_mini_workshop directory is called workshopTraining",

  # explanation_5
  "**`[username\\@submit002 ~]$ cd workshopTraining`**\n\nResult: [username\\@submit002 workshopTraining]$ Notice ~ was in the home directory, now in the workshopTraining directory.",

  # explanation_6
  "**`[username\\@submit002 ~]$ rm -r TaskProject`**\n\n*Note: -r means directory\n\nResult: TaskProject is deleted",

  # explanation_7
  "**`[username\\@submit002 ~]$ cp -r Task1 Project`**\n\nResult: Task1 directory has moved to the Project directory.",

  # explanation_8
  "**`[username\\@submit002 ~]$ find Project`**\n\nResult: Task1 will appear within the Project directory\n\nProject\nProject/Task1",

  # explanation_9
  "**`[username\\@submit002 ~]$ head -n5 file_name`**\n\nResult: It will display the first 5 lines from the beginning of the file_name.",

  # explanation_10
  "**`[username\\@submit002 ~]$ tail -n5 file_name`**\n\nResult: It will display the last 5 lines from the end of the file_name",

  # explanation_11
  "**`[username\\@submit002 ~]$ less file.txt`**\n\nResult: The user is able to view a portion of the file.txt.",

  # explanation_12
  "**`[username\\@submit002 ~]$ more file.txt`**\n\nResult: The user is able to view the entire file.txt.",

  # explanation_13
  "quit viewing the current file",

  # explanation_14
  "**`[username\\@submit002 ~]$ cat file.txt`**\n\nResult: Display the contents of file.txt",

  # explanation_15
  "**`[username\\@submit002 ~]$ grep “GCGGA” sequence_file.fastq`**\n\nResult: Display any GCGGA pattern in sequence_file.fastq",

  # explanation_16
  "**`[username\\@submit002 ~]$ wc file.txt`**\n\nResult: Display the number of words, lines, and characters in the file.txt.",

  # explanation_17
  "**`[username\\@submit002 ~]$ touch exampleFile.txt`**\n\nResult: The command line will display file details in
  the current directory"
  ))

# Apply formatting to the Command_Line column
#commands$Command_Line <- cell_spec(commands$Command_Line, "html", font = "Courier", color = "black", background = "lightgray", escape = FALSE)

knitr::kable(
  commands,
  format = "html",
  col.names = c("Name", "Command Line", "Description", "Example"),
  align = c("l", "l", "l", "l"),
  escape = FALSE
) %>%
  kable_styling() %>%
  # Set background color for alternating rows
  row_spec(seq(2, nrow(commands), 2), background = "#e9f5f8")

```