search

usegalaxy-eu / usegalaxy-eu-tools

List of tools included in https://usegalaxy.eu
MIT License
26 stars 125 forks source link

OpenMS tools not updated #582

Open bernt-matthias opened 1 year ago

bernt-matthias commented 1 year ago

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

xref https://github.com/usegalaxy-eu/usegalaxy-eu-tools/issues/339?

bgruening commented 1 year ago

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 commented 1 year ago

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

added:

removed:

bernt-matthias commented 1 year ago

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 commented 1 year ago

Found the error, will try to fix it.

bgruening commented 1 year ago

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

hechth commented 10 months ago

@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 commented 10 months ago

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 https://github.com/galaxyproteomics/tools-galaxyp/pull/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.