OpenMS tools not updated

[bernt-matthias]

All seem to be at 2.6 .. latest is 2.8.

xref #339?

[bgruening]

Mh wired they are part of the galaxy file, which is trusted and should get auto installed. That a single tool is missing can happen, we still need to add new tools to the yml file. But the updates should happen :-(

[bernt-matthias]

With the 2.8 update there have been only a few changes in the set of tools:

added:

• OpenMSDatabasesInfo
• TriqlerConverter

removed:

• FeatureFinderSuperHirn

[bernt-matthias]

According to the lock file for openms_msfgplus... we have

  - 2e87a752617e	11
  - a407b6790342	5
  - bf88d58b098c	13
  - c18d8efa4474	14
  - e3310bcd96d7	12
  - f5ec766d80cf	15

The numbers at the end are the numbers shown in the TS and 15 should be the latest version f5ec. But installed are only 5 versions and the latest (v2.8) is missing.

[bgruening]

Found the error, will try to fix it.

[bgruening]

Ok msgfplus is now available and I hope the install script will fix the rest automatically over the weekend.

[hechth]

@bernt-matthias what happened to the superhirn tool? Also, what is up with the FeatureGrouping set of tools which are available using pyOpenMS? Are there some Galaxy equivalents for those?

[bernt-matthias]

what happened to the superhirn tool?

Has been removed from OpenMS in 2.7 https://github.com/OpenMS/OpenMS/blob/0b6c4dbe9b8a651c6030fb6c9f7a2d0ac613d148/CHANGELOG#L184C3-L184C25

what is up with the FeatureGrouping set of tools which are available using pyOpenMS? Are there some Galaxy equivalents for those?

Currently only binaries shipped with OpenMS are wrapped. Do you have links to the tools that are missing?

Maybe lets continue for new tools that are missing over here galaxyproteomics/tools-galaxyp#697 .. hopefully I can find some time to work on 3.0 soonish ..

For this issue the open question is how to deal with deprecated tools.