On Mon, Oct 22, 2012 at 4:23 PM, David Hoover <hoove...@helix.nih.gov> wrote: > How does Galaxy determine that a job has failed?
It now depends on the individual tool's XML file. > Does it simply see if the STDERR is empty? Why default, yes. The tool's XML can specify particular regexs to look for, or to decide based on the return code - but for the time being most of the tools still just look at stderr. See: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax > What happens if an application normally outputs to STDERR? Either use the new functionality in the XML definition, or what older Galaxy tools did was a wrapper script to hide/redirect stderr to avoid false positives. > This is a problem for our local installation, as I have enabled it to > run as the local user on the backend cluster. If a user has an > error in the .bashrc file, it will automatically write to STDERR, > and all jobs, no matter what, are labelled as failing. In which case the user should see those errors and be able to do something about it, right? Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/