gotcloud Print errors/warnings to STDERR/STDOUT

Please print out any warnings/errors to STDOUT/STDERR in addition to any .err files.

Nov 17 '15 20:11 schelcj

If runcluster.pl detects a .err file, it can print it to STDERR. make will send that through to its STDERR, which is otherwise clean.

Do you log the Makefile's STDERR to a file? Is that good enough? Or do we need to keep passing it up the chain?

Nov 17 '15 21:11 pjvandehaar

Main problem is seeing a message after alignment error to look for Makefile.err. Would be useful to see that output on STDERR. In a scheduler, pbs/slurm, it will be in the jobs output file.

Nov 17 '15 21:11 schelcj

Try https://github.com/statgen/gotcloud/tree/b6cfcdc (which is on branch peter-develop just ahead of master)

Nov 17 '15 22:11 pjvandehaar

Ah, got it, you're running gotcloud locally. This issue will become much nastier with a cluster.

Nov 18 '15 01:11 pjvandehaar

Is this solution working for you?

Dec 15 '15 21:12 pjvandehaar

Sorry, no, I haven't been able to switch to a dev branch on these runs.

Dec 16 '15 12:12 schelcj

I've merged that commit into master now, so whenever you update it should be ready.

Dec 16 '15 13:12 pjvandehaar