Galaxy interprets logger output to stderr as an actual error

[matnguyen]

Since Galaxy interprets any output to stderr as an error, even though pathogist works fine, the galaxy output will be red and indicate that an error occured.

Make the logger output to stdout to fix this issue.

[sean-la]

Is it sufficient to have it as an option to output logger to stdout? If I make it only go to stdout, we lose time information.

[matnguyen]

As long as there is no output to stderr when that option is selected, it will work with Galaxy.