Versions Compared

Old Version 9

changes.mady.by.user Deatherage, Daniel E

Saved on

compared with

New Version 10

changes.mady.by.user Deatherage, Daniel E

Saved on

Key

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

...

If you run the which command above outside of an idev session you should see 2 results. If you run from inside an idve node you get 1 result. On the head node (outside idev) 1 that points to the BioITeam near where you keep finding your data (/corral-repl/utexas/BioITeam/) part of the answer as the BioITeam. The "bin" folder specifically is full of binary or (typically small) bash/python/perl/R scripts that someone has written to help the TACC community. The other is in a folder specifically associated with the bioperl module.


Info
titleWhy do you get 2 different results depending on if you are inside or outside of an idev node

This has to do with how compute nodes are configured. On stampede2 /corral-repl/ and all of its subdirectories are not accessible so even though the BioITeam is in your $PATH, on the compute node, the command line can't access it. This is why in later tutorials you have to log out of the idev session to copy new raw data files to work with.

If you try to run the BioITeam version of the script from the head node /corral-repl/utexas/BioITeam/bin/bp_seqconvert.pl , you get the following error message:

...