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usegalaxy-no / galaxyadmin

A repository for managing the work of the usegalaxy.no GalaxyAdmin team
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Problems with data types #13

Closed ehj000 closed 3 years ago

ehj000 commented 3 years ago

The tool EDGE-pro Gene expression in Prokaryotes (Galaxy Version 1.0.2) requires the two "non-standard" data types "ptt" and "rnt". They have been added to usegalaxy (by Kjetil?), and they appear both in the list of usegalaxy.no data types and are possible to select when using the tool. Nevertheless, the tool fails with the following error: tool error An error occurred with this dataset: cannot find 'settingsType' Would be nice if someone could look at this

kjetilkl commented 3 years ago

The problem is in the wrapper itself. The execution command (cheetah template) references the parameter "settingsType", which was present in an earlier version of the tool but has been removed in version 1.0.2. I have made an updated version of the wrapper in the NeLS Toolshed which no longer references this parameter (it is not strictly needed).

I also removed the two datatypes "ptt" and "rnt" from the wrapper, since installation of new datatypes from toolsheds has apparently been deprecated. Also, I am not sure that it actually works. Our test server has the same tool wrapper installed, but it does not have the "ptt" and "rnt" data types. We could add these two datatypes to a local configuration file instead with Ansible.