Overview:

Lonestar is tremendously powerful and capable of doing many things, but as most of you are probably being slightly frustrated by, it doesn't have much in the way of a GUI (graphical user interface). The lack of a GUI means it can't visualize graphs or other meaningful representations of our data. In order to do these types of things, we have to get our data off of lonestar and onto our own computers.

You recall one of the first things you did in this class was use the cp command to copy files from the the BioITeam directories to your home directory. Unfortunately lonestar can't access the directories on your personal computer so the cp command won't work. Instead we have to use the "secure copy command" (scp). Copying using  scp works using the same 3 parts as the cp command:

1. the command itself (now scp instead of cp)
2. The file you want to securely copy 
3. The location you want the new file to go to

The difference is the scp command includes more detailed information on the path of where the file is, or where the file is going using syntax similar to that used in the other "secure" command you are familiar with: ssh.

Objectives:

1. Transfer a file from ls5 to your local computer.
2. Transfer a file from your local computer to ls5.

Tutorial:

• Setup

It is often useful to set up 2 different terminal windows to scp between a remote computer and your local computer. This is not required by any means, but is often helpful. The image below shows 2 separate windows where I have transferred a file named README from a folder inside the BioITeam materials to my local computer. Notice the one on the left corresponds to my local computer while the other is actually inside of the BioITeam folder on TACC. 

• Transfer from ls5 to your computer

Before you begin, be sure you have 2 terminal windows open as shown above. For simplicity the window corresponding to your Local computer will be referred to as "Left" while the window where you have logged into the Remote computer will be referred to as "Right" as is depicted in the image above.

In the Right window (Remote):

1. Navigate to the directory that contains the file you want to transfer.

   cd /corral-repl/utexas/BioITeam/ngs_course

2. Use the pwd command to print the current working directory

   pwd

3. Copy the address by highlighting the text and hitting control/command + C

   Explaining why this 'recommended practice' isn't actually necessary.

   Note that if you are sure you know the address your file resides at from root, you do not need to do this step, but in the experience of your instructor, being able to type the address out with tab keys in the remote window will safe a lot of typos when the next steps are completed.

In the Left window (Local):

1. Navigate to the directory that you want to copy the file to.

   cd Downloads

2. The scp command will have the following parts: scp <USERNAME>@<Remote_computer_address>:<pathway_to_file_you_want_to_transfer_starting_with_a_/_mark_and_ending_with_the_filename> <location_you_want_the_file_copied_to>

   use the scp command to transfer the remote file to to your local computer

   scp <USERNAME>@ls5.tacc.utexas.edu:/corral-repl/utexas/BioITeam/ngs_course/README . 

   *note the required punctuation:

   1. @ symbol following your username (same as is done in the ssh command)
   2. : following the remote computer address. Missing this mark is the 2nd most common mistake people make
   3. / immediately after the : mark. Missing this mark is the most common mistake people make.
   The final . on the command is not a required piece of punctuation, but instead is the symbol for the current directory. Step 1 could have been skipped, and the "." replaced with "Downloads" to have the same effect.

3. Upon hitting enter you should be prompted for your tacc password, and 1 time code.

• Transfer from your computer to ls5

Alternatives:

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