[Owl-devel] TcoffeeRunner bug

Jose M. Duarte jose.m.duarte at gmail.com
Wed May 19 12:29:26 EDT 2010

Hi all

I've just fixed a bug with TcoffeeRunner apparently due to a different
behaviour in recent versions of t_coffee. I'm using 8.14 (but over there you
guys seem to have 5.05)

The problem was that the t_coffee process was hanging after spawning.
Basically t_coffee seems to be doing something weird with stderr and stdout,
java doesn't like it and makes the process hang. As usual java has a lot of
problems in this area, see owl.core.util.StreamGobbler class (that caused a
lot of headaches with CMView).

The way to solve it is use the -quiet switch of t_coffee so that the output
can be redirected to a file (to log as before) or have a complete quiet
terminal and no logging.

This might affect the CASP code, that's why I'm warning you guys....
Basically if the code doesn't work anymore you will have to upgrade to
latest t_coffee (which anyway is a good idea as that version is more than 2
years old)


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