2.2 Getting organized

From this point we’ll use line commands. Some steps might be feasible with the mouse, but I encourage you to use the command-line, even for a simple thing as creating a new directory⁶.

TASK
Open a text Terminal and follow instructions below:

1. Start Terminal: (see section 1.3.)
   
2. Terminal will look within your User directory by default (e.g. /Users/jsgro for me.) This is your default “home” directory.
3. If you want to save your project elsewhere, first change to that location, e.g. cd Desktop:

cd ~/Desktop

3. Create a new directory:

mkdir spike

4. Change into this directory:

cd spike

5. Move the saved sequence file saved with the browser here. By default the file would be saved in the Downloads folder of your user area. Of course if your browser saved the file elsewhere then adapt to that location. You can take this opportunity to rename the file while moving it from its download location.

Since there were 85 files we could choose e.g. spike_85.fa but most likely this number will evolve with time. So perhaps spike_raw.fa would more generic and endure better with time. (See update in section 2.1.)

mv ~/Downloads/sequence.fasta.txt spike_raw.fa

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6. “Directory and Folder” are equivallent.↩︎

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