Executable in clustalw 2.x package is named clustalw When using bioperl-run test suite it is uncovered that t-coffee is wrongly seeking for a clustalw2 executable. A patch is applied to rather seek for clustalw.
increase MAX_N_PID to Linux 64 bits theoretical maximum Since Debian Bullseye, the system now has a default pid_max of 4194304 instead of the historical 32768. This renders t-coffee much more likely to crash on compute nodes always powered on in computer centers. This patch addresses that issue with a value set to the theoretical upper limit of Linux on 64 bits systems.
Fix Mayhem issue The idea behind this patch is that if there is a problem to set the HOME directories no additional processes can exist and so we should *really* exit. Somehow the printf_exit() function does some logic which ends up in an endless loop and thus forcing the exit will help here.
