Hi all<br><br>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)<br><br>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).<br>
<br>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.<br><br>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)<br>
<br>Cheers<br><br>Jose<br><br>