Versions Compared

Old Version 8

changes.mady.by.user Deatherage, Daniel E

Saved on

compared with

New Version 9

changes.mady.by.user Deatherage, Daniel E

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

Expand
titleHere are the commands we showed you for the previous example (with the trick of getting a single compressed output directory you just learned) to transfer so you don't have to scroll back and forth. See if you can remember how to do it without going back over the lesson.

To use scp you will need to run it in a terminal that is on your desktop and not on the remote TACC system. It can be tricky to figure out where the files are on the remote TACC system, because your desktop won't understand what $HOME, $WORK, $SCRATCH mean (they are only defined on TACC).

To figure out the full path to your file, you can use the pwd command in your terminal on TACC in the window that you ran breseq in (it should contain an "output" folder). Rather than copying the entire contents of the folder which can be rather large, we are going to add a twist of compressing the entire folder into a single compressed archive using the tar command so that the size will be smaller and it will transfer faster:

Code Block
languagebash
titleCommand to type in TACC
tar -czvf output.tar.gz output_*/output  # the czvf options in order mean Create, Zip, Verbose, Force
pwd

Then you can then copy paste that information (in the correct position) into the scp command on the desktop's command line:

Code Block
languagebash
titleCommand to type in the desktop's terminal window
scp -r <username>@lonestar.tacc.utexas.edu:<the_directory_returned_by_pwd>/output.tar.gz .
tar -xvzf output.tar.gz  # the new "x" option at the front means eXtract

...