Logging when dealing with temp paths.

[jfear]

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.

1. should we attempt to get the wrappers working most efficiently for our use case (i.e. biowulf and /lscratch).
2. When a tool dumps to cwd what should our SOP be.
3. 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.