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setup.md

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Setup
/setup/

We are going to download some files into our personal "home" directories on Palmetto from the web. The data is in the form of a .zip file which can be found at the following URL.

https://github.com/clemsonciti/genomics-workshop/raw/gh-pages/data/genomics-workshop.zip

Because we can't run a graphical web browser on the cluster, we need another way of downloading the .zip file. Fortunately, there is a command-line tool called wget that is meant for exactly this task.

[nelle@login001 ~]$ wget https://github.com/clemsonciti/genomics-workshop/raw/gh-pages/data/genomics-workshop.zip

{: .bash}

[nelle@login001 ~]$ unzip genomics-workshop.zip
Archive:  genomics-workshop.zip
   creating: genomics-workshop/
   creating: genomics-workshop/shell-basics/
   creating: genomics-workshop/shell-basics/data/
   creating: genomics-workshop/shell-basics/data/molecules/
  inflating: genomics-workshop/shell-basics/data/molecules/cubane.pdb
  inflating: genomics-workshop/shell-basics/data/molecules/ethane.pdb
  inflating: genomics-workshop/shell-basics/data/molecules/methane.pdb
  inflating: genomics-workshop/shell-basics/data/molecules/octane.pdb
  inflating: genomics-workshop/shell-basics/data/molecules/pentane.pdb
  inflating: genomics-workshop/shell-basics/data/molecules/propane.pdb
   creating: genomics-workshop/shell-basics/data/pdb/
.
.
.

{: .output}

Once you have downloaded the .zip file, you may "unzip" it using the unzip command:

[nelle@login001 ~]$ unzip genomics-workshop.zip

{: .bash}

[nelle@login001 ~]$ unzip genomics-workshop.zip
Archive:  genomics-workshop.zip
   creating: genomics-workshop/
   creating: genomics-workshop/shell-basics/
   creating: genomics-workshop/shell-basics/data/
   creating: genomics-workshop/shell-basics/data/molecules/
  inflating: genomics-workshop/shell-basics/data/molecules/cubane.pdb
  inflating: genomics-workshop/shell-basics/data/molecules/ethane.pdb
  inflating: genomics-workshop/shell-basics/data/molecules/methane.pdb
  inflating: genomics-workshop/shell-basics/data/molecules/octane.pdb
  inflating: genomics-workshop/shell-basics/data/molecules/pentane.pdb
  inflating: genomics-workshop/shell-basics/data/molecules/propane.pdb
   creating: genomics-workshop/shell-basics/data/pdb/
.
.
.

{: .output}

Confirm that a new folder genomics-workshop has been created as a result of extracting the genomics-workshop.zip file:

[nelle@login001 ~]$ ls

{: .bash}

genomics-workshop  genomics-workshop.zip

{: .output}