...

Before you begin, be sure you have 2 terminal windows open as shown in the "setup" section 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.

...

1. Code Block
   language bash title Navigate to the directory that contains the file you want to transfer.
   cd /corral-repl/utexas/BioITeam/ngs_course

2. Code Block
   language bash title Use the pwd command to print the current working directory
   pwd

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

   Info
   title Explaining why this the 2 window 'recommended practice' isn't actually necessary.
   Note that if If you are sure you know the address your file resides at from root, you do not need to do this step, but in . 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.

...

1. Code Block
   language bash title 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>

   Code Block
   language bash title 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.

   Info
   title

   The final .

   Explaining why this is the only actual required command

   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.

4. You can then navigate to that folder using your operating system to see the new file and choose what to open it with (in this case it is a text file)

• Transfer from your computer to ls5

Before you begin, be sure you have 2 terminal windows open as shown in the image in "setup" section 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. Code Block
   language bash title Navigate to the directory that you want to transfer the file to..
   cd $SCRATCH

   Warning
   title Please do not upload files to the BioITeam folder
   In the previous example we copied a file from the BioITeam to your local computer. Make sure you change your directory before copying a file back to TACC. If you copy a file into that BioITeam space it creates more work for your instructor of having to clear out that space.

2. Code Block
   language bash title Use the pwd command to print the current working directory
   pwd

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

   Info
   title Explaining why the 2 window 'recommended practice' isn't actually necessary.
   If you are sure you know the address your file resides at from root, you do not need to do this step. 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. Code Block
   language bash title Navigate to the directory that has the file you want to copy.
   cd Downloads

2. The scp command will have the following parts: scp <filename> <USERNAME>@<Remote_computer_address>:<location_you_want_the_file_copied_to_starting_with_a_/_mark>

   Code Block
   language bash title use the scp command to transfer the remote file to to your local computer
   scp README <USERNAME>@ls5.tacc.utexas.edu:<pwd_you_copied_in_the_right_window> .

   *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.

   Info
   title

Alternatives:

...

1. Explaining why this is the only actual required command

   As above, if you know the path to the directory you want to copy your file to, you do not need the Right window with the remote connection. Unfortunately, just as the remote computer doesn't know anything about your local computer, your local computer doesn't know anything about the nice shortcuts that exist on TACC such as the $SCRATCH variable. This means that in order to do this with a single window you would need to know what $SCRATCH is from memory. Even assuming you did know the path to the directory you want, it has been extremely rare in my experience that transferring a file to TACC is the last step. Almost always it is actually the first step where once the file is transferred you immediately begin working on it there.

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

3. Switch back to the other window and use the ls command to see the file.

Alternatives:

While you can return to Genome Variant Analysis Course 2020 Home Page, it is more likely that you want to use the back arrow on your browser to return to the page you were just on.