snpSift_filter tool

[tothuhien]

The tool failed with error missing Java

[sveinugu]

@kjetilkl Did you just fix this (ref. Slack)?

[kjetilkl]

I believe I have fixed it for now, but I noticed that this issue is exactly the same as issue #43, which we solved back in April last year. Part of that solution was to uninstall the SnpSift Filter versions that did not work, but either we forgot to do that or these versions have since been installed back again because they are part of some lists that control automatic tool installation (see here and here). I suggest we keep this issue open for now and revisit it in a few weeks to see if the faulty tool versions have come back.

[kjetilkl]

After we uninstalled the SnpEff tool suite version 3.4 yesterday, we have had 10 jobs for 5 different tools that all have failed with the same error message: ModuleNotFoundError: No module named 'galaxy.datatypes.snpeff'

The SnpEffDb datatype, which is used by these tools (a subtype of Text, aka "txt"), was included in first revision of this tools suite in the wrapper file lib/galaxy/datatypes/snpeff.py, but it has since been removed from the wrapper and is now part of the standard Galaxy codebase in the file /srv/galaxy/server/lib/galaxy/datatypes/text.py instead. This meant that we have had two parallel datatypes called SnpEffDb, namely galaxy.datatypes.snpeff:SnpEffDb and galaxy.datatypes.text:SnpEffDb. After I restarted the Galaxy server at 3 PM today, only the latter now remains.

I don't know what to do about these errors, or if they even are errors anymore. Maybe they will now magically disappear on their own if the users simply rerun the failing jobs or change the datatype of their datasets to "snpeffdb". I least I'm not keen on bringing back the old galaxy.datatypes.snpeff module from the wrapper.