ganon build-custom prints an interactive message from seqan causing 'hanging' in non-interactive compute environments

[jfy133]

I was just testing ganon custom-build (finally back to it after parental leave), and when running it on a HPC my job hung.

I later found out it was because it was waiting for a response to this question:

#######################################################################
   Automatic Update Notifications
#######################################################################

 This app can look for updates automatically in the background,
 do you want to do that?

    [a] Always perform version checks for this app (the default).
    [n] Never perform version checks for this app.
    [y] Yes, perform a version check now, and ask again tomorrow.
    [s] Skip the version check now, but ask again tomorrow.

 Please enter one of [a, n, y, s] and press [RETURN].

 For more information, see:
 https://docs.seqan.de/sharg/main_user/about_update_notifications.html

#######################################################################

n

I think that's from a upstream dependency, but this is not very nice when working in non-interacive contexts...

Apparently you can turn this off via a seqan command: as listed here: https://docs.seqan.de/sharg/main_user/about_update_notifications.html#autotoc_md7

I think it might be good to have that included in ganon if I understand this issue correctly

[pirovc]

Thanks for reporting @jfy133, good to have you back :)

I agree with you and this shall be removed in the next patch.