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Week 2 Outline

Review

  • Introductions
  • Syllabus Overview and Questions
    • Assignments due Fridays at noon each week.
    • Class will focus on pragmatics of computing.
    • Plagiarism
      • Searching for solutions online will probably be necessary at some point, but credit must be given.
  • The Linux Virtual Machine
    • May be easiest to run directly off of flash drive or OneDrive
    • For flash drives that move b/w Windows and Mac, will need to have FAT32 format and will need to reduce memory size of VM
  • Markdown and Outlines
    • Can take notes directly in file - maybe use block quotes?
    • In Atom, install these packages:
      1. markdown-preview
      2. language-markdown
      3. Toggle preview on and off with Shift-Ctrl-M

This is a block quote. This might be an easy way to add your own notes.
To write notes on new lines, add two empty spaces or <br> at the end of a line.

  • GitHub and Homework
    • Repositories
      • Collections of related files (often code)
      • Formalizing as a repository allows Git to keep track of changes you make in these files through time
      • You can also copy someone else's repository (fork), make your own changes (commits), then ask the original owner to include your changes (pull request)
    • Pull Requests
      • Can also use these to share notes
GitHub exercise

1. Go to the `week 2` repository on the class GitHub page
2. Click the `fork` button in the upper-right of the page
3. Go to your newly forked copy of the repository
4. Add your name here:
	- Adora
	- Willie Hurst
	- Jeremy
	- Ruth
	- Zara
	- Gentry
	- Eric
	- Jacob
	- Cameron
	- Megan
	- Ethan
	- Devin
	- Charis
	- Lane H. Bazar
	- Caroline Kaufman 
  - Adam 
5. Create a pull request
6. Add a commit message to your request to indicate the change you made
7. Submit your pull request

Filesystem Structure

  • Review last week's exercise
    • Recreate files and folders, if necessary
 ~/Desktop/Biology/
				README.txt
				CellBiology/
					ImportantCellBioTopics.txt
				Ecology/
					ImportantEcolTopics.txt
				Evolution/
					ImportantEvolTopics.txt
					Phylogenetics/

pwd will tell current working directory

absolute path to phylogenetics: cd /home/compbio/Desktop/Biology/Evolution/Phylogenetics/

back to home user: cd ~

relative path: cd Desktop/Biology/Evolution/Phylogenetics cd ./Desktop/Biology/Evolution/Phylogenetics

ls will list ls - a will show hidden files (has . .. which are references to where you are and the parent folder)

~ will put you at user level

  • The Unix root (/)
    • The very base of the filesystem
  • Absolute paths
    • All absolute paths begin at the root- start with /
  • Relative paths
    • dont start with /
    • Working directories
    • Shortcuts for current and parent directories
  • Hidden files and folders
    • Names begin with .
    • Usually used for configuration files
Filesystem Exercise

1. Based on the directory structure above, find the Population Genetics folder.
2. Write the absolute path to that folder.
3. If Population Genetics is your working directory, write the relative path to the Phylogenetics folder.
4. If Biology is your working directory, write the relative path to Phylogenetics

Practical Computing Advice

  • Naming files and folders
    • CamelCaseLooksLikeThis
    • underscores_can_work
    • NEVER use spaces!! Spaces confuse terminal
    • Generally a good idea to avoid special characters
  • Plain text files
  • New line characters
  • Activity Monitor
    • CPU Activity
    • Memory
    • Disk spaces
    • Jobs and IDs

Introduction to the Command Line

  • Terminal
    • Built in to Linux (and Mac OS X)
    • By default, uses the bash shell (interpreter)
    • The command prompt
    • Tab completion
    • double tap tab will list all files with that beginning
    • Scrolling through history
  • Commands related to navigating the filesystem
    • 'touch filename.txt' will create file
    • pwd - print working directory - or - "where am I?"
    • ls - list directory contents
      • 'ls -l' - long list
        • Everything has three types of permissions
          • Read
          • Write
          • Execute
        • And three groups whose permissions can be controlled
          • Owner
          • Group
          • Others
        • Wikipedia on Unix Permissions
      • la - list with hidden files
    • cd - change directory
      • will accept absolute or relative paths
    • chmod - change permissions - specify who (ugo), how (+ or -), and what (rwx)
    • man <command> - gives us the manual page and options for any Unix command (q will get out of manual page)
First Command-Line Exercise (add commands run as notes as you go)

1. Change directories to the Desktop
2. List the visible contents of the directory
3. Now list _all_ contents of the directory (including hidden files and folders)
4. Chage directories to your home directory (remember the shortcut)
5. List the visible contents of the directory
6. List all contents of the directory
  • Commands related to files and folders

    • cp - copies a file

      • cp originalFile.txt newFile.txt

    • mv - moves or renames a file

      • To change location, use paths: mv myFile.txt ./folder/myFile.txt
      • To change name, just use different names: mv myFile.txt newName.txt

    • cat filename.txt - view file contents - can be called on multiple files and will conCATenate their contents

    • 'cat file1.txt file2.txt file3.txt' will show all files in command line

    • 'cat *.txt' shows all text in files with the file ending .txt

    • 'ls *.txt' show all files that end in .txt

    • 'ls ../*.txt' go up one directory then tell me the txt files there (still within the same directory)

    • can add file/filename.txt in nano

    • head -n # - view the first # of lines of a file

    • tail -n # - view the last # of lines of a file

    • less - view the contents of a file a little at a time nice way to scroll through

    • touch filename.txt - quickly create a new file

    • nano filename.txt - this is actually an entire text editing program (type text like normal)

    • 'write out is save' and ^=control (^O) exit (^X)

    • wc - print out the length of a file in lines, words, and characters

    • >> - appends to file

      • echo "some text here" >> myTextFile.txt

    • > - writes to (or over!) file

      • echo "more text here" > myTextFile.txt

    • WARNING - BIG WARNING - PAY ATTENTION - rm permanently removes a file

      • No going back - always use this VERY carefully
      • I know people who've accidentally erased their entire computers using this command
        • rm -r recursively removes a directory and everything inside it - even more dangerous than just rm!
      • This is the reason permissions are so important. If someone doesn't have write permissions on a file or folder, they shouldn't be able to delete it.

    • mkdir MyDirectory - create a new (empty) directory (folder)

    • rmdir MyDirectory - remove an empty directory !!WARNING!!

    • wildcards - * is especially useful - matches anything

    • grep - find only lines matching some particular string

    • 'cp filename.txt filename2.txt' will copy contents

    • 'mv filename filename' will change name of file

    • 'mv filename ./Biology/' will move file name into folder that is in current working directory or without './' will work too

    • Commands related to the Unix environment

      • Can create a variable and assign value using =
        • myVariable=2
      • Can print value of variable using echo and starting name with $
        • echo $myVariable
      • | - the Unix pipe can be used to send the output of one command into the input of another
        • history | tail -n 20 >> endOfHistory.txt

Week 2 Assignment (Due. Fri, Aug. 31, at NOON)

  1. Using the mkdir, touch, echo, and/or nano commands, recreate the directory and file structure above.
  2. Using cd with an absolute path, change your working directory to phylogenetics.
  3. Using nano, create and save a new text file with your favorite phylogenetic fact (e.g., "Birds are actually descended from dinosaurs!"). Feel free to search online, if you don't have one ready.
  4. Using cd with a relative path, change directories to Biology.
  5. Using ll or ls -l, list the contents of Biology and send it to a new file called BioContents.txt.
  6. Now, carefully delete the Cell Biology folder and any files it contains.
  7. Using history, a pipe, and tail, create a file (myCommands.txt) that shows the history of commands you ran for steps 1-6.
  8. On GitHub, fork the week2 repository.
  9. On your computer, create a folder with your name and put the entire Biology directory hierarchy inside it.
  10. While looking at your fork of week2 on GitHub, go to the week2Assignments folder, click the Upload files button in the upper right, then upload the directory with your name by dragging and dropping. Add a commit message and commit the new files and directories.
  11. After committing the new files, submit a pull request to the class page.