One issue I ran into with rseqc is that some of the tools just dump output to cwd. For cluster use it would be best to do all of this in /lscratch and move the files after words. It is easy enough to change inputs to absolute paths, but changing the log is more difficult when using your log fmt method. I guess the question is several parts.
- should we attempt to get the wrappers working most efficiently for our use case (i.e. biowulf and
/lscratch).
- When a tool dumps to
cwd what should our SOP be.
- Depending on (1) and (2) if we need to mess with the path of log should we just hard code it to the wrapper or should we come up with a patch to your log fmt.
One issue I ran into with rseqc is that some of the tools just dump output to
cwd. For cluster use it would be best to do all of this in/lscratchand move the files after words. It is easy enough to change inputs to absolute paths, but changing the log is more difficult when using your log fmt method. I guess the question is several parts./lscratch).cwdwhat should ourSOPbe.