Update comet executable to 2023 version

[jonasscheid]

According to #97

[timosachsenberg]

@jpfeuffer Jonas downloaded it from the release page. I think the comet guys build on Ubuntu. Size looks like it could be static. Could this work? @jonasscheid If so, we probably should also add the executables for mac and win

[jonasscheid]

Actually I cloned the comet repo and built the executable from source. I could also exchange the executable with the ones comet provides. Let me check if that one works on my ubuntu instance

[jpfeuffer]

I am not sure how much of the selfbuilding is needed these days. It should be a standalone executable if possible and built against a low enough Glibc/macOS SDK such that it runs on the same OS versions that we support with the OpenMS tools. Windows should not be an issue these days, as long as they keep their ABI compatibility in the VS Redistributables.

Which executable platforms can be downloaded @jonasscheid ?

[timosachsenberg]

https://github.com/UWPR/Comet/releases/tag/v2023.01.0 but the actions look like they use only -latest systems: e.g. https://github.com/UWPR/Comet/blob/master/.github/workflows/linux-build.yml

[jpfeuffer]

Hmm yes this might be a problem.

[timosachsenberg]

what would be alternatives?

• taking the github action from comet and setting the OS to the lowest possible version? btw I wrote an issue in the comet repo. Maybe they could do that (if it helps).

[jpfeuffer]

For Ubuntu that works (although some kind of manylinux is of course preferable). For macOS one should additionally set the MACOS_DEPLOYMENT_TARGET to a low version (maybe 10.15 these days)?

[jonasscheid]

Also worked for me on ubuntu 👍

[jpfeuffer]

which Ubuntu version do you have?

[jonasscheid]

Recompiled from source on Linux 5.4.0-65-x86_64 with:

ldd (Ubuntu GLIBC 2.31-0ubuntu9.7) 2.31

g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0`

-> 20.04.1

[jpfeuffer]

Okay. 20.04 with glibc 2.31 is fine.

[poshul]

If we only need the MacOS version now to proceed (with Windows working, and @jonasscheid's Linux version compatible with 20.04) Is it worth just building the MacOS version on Abibuilder and including that?

[jpfeuffer]

Yes, that will work. As expected, I get:

dyld: Symbol not found: __ZTTNSt3__114basic_ifstreamIcNS_11char_traitsIcEEEE
  Referenced from: /Users/pfeuffer/Downloads/comet.macos.exe (which was built for Mac OS X 12.0)
  Expected in: /usr/lib/libc++.1.dylib
 in /Users/pfeuffer/Downloads/comet.macos.exe
[1]    23267 abort      ~/Downloads/comet.macos.exe

with the provided version. Since I am on 11.7.3

[jonasscheid]

Would this new release of comet fix the problems with your Mac version @jpfeuffer? https://github.com/UWPR/Comet/releases/tag/v2023.01.1

It also fixed a (I would say crucial bug for us as well https://github.com/UWPR/Comet/issues/33)

[jpfeuffer]

Macos 11 should be fine. I did not test yet but I am also currently hacking my Mac to make it install a newer OS.

[cbielow]

The latest release seems to have major bug (see Comet Mailing list). Jimmy is usually very fast to fix those and publish a new release, but we should not ship the current version.

[jonasscheid]

Another one? Or do you mean this one https://github.com/UWPR/Comet/issues/33

[jke000]

The latest release seems to have major bug (see Comet Mailing list). Jimmy is usually very fast to fix those and publish a new release, but we should not ship the current version.

@cbielow, is the major bug the missing support for mzML/mzXML files that don't have the optional scan indexes? The Comet google group has been pretty quiet so this must be it but I want to make sure I address all open issues before I make the next release.

[cbielow]

The latest release seems to have major bug (see Comet Mailing list). Jimmy is usually very fast to fix those and publish a new release, but we should not ship the current version.

@cbielow, is the major bug the missing support for mzML/mzXML files that don't have the optional scan indexes? The Comet google group has been pretty quiet so this must be it but I want to make sure I address all open issues before I make the next release.

Yes indeed. That was the issue i was referring to.

[jonasscheid]

New Comet release is there! I uploaded the executables. There is now a hidden parameter export_additional_pepxml_scores (for us) to obtain additional features that are already contained in the pin file 🤙🏼 Thanks to @jke000 for the quick release