GTN for GC-MS processing with metaMS on Galaxy

[jsaintvanne]

Just a new tutorial for GC-MS datas with metaMS package.

@yguitton @lecorguille

[shiltemann]

Welcome @jsaintvanne! And thanks for contributing, please let us know if there is anything we can help with!

[melpetera]

The error in the checks is out of my league. I guess it may be linked to the fact that this PR is quite old, but that is only random guess. A little help from someone more experienced in GTN materials is welcome here.

[melpetera]

Hum, I was advised to do a rebase here because the fact that tests did not pass was potentially due to the PR being very old, but I may not have done things the better way here, since now the PR seems to integrate all the commits from a year and a half of main... Well, the checks are indeed all green now, but the actually changed files seem now invisible among the 1800+ commits corresponding to a merge of the main inside this old branch... Sorry for the mess :confounded:

[gallardoalba]

Hi @melpetera, you have included the .github folder in the PR; you need to remove it.

[hexylena]

I think it might be more than that, I'm not sure why GH is shown this in the files changed tab when clearly the main branch was just merged in

[hexylena]

@melpetera could you list the files that were intended to be part of this PR, maybe one of us can have another attempt at the rebase to clear up what's actually changing

[melpetera]

Hi and thank you for your time.

As it is a new tutorial, what have been actually changed in this PR is the following:

• all files in the "topics/metabolomics/tutorials/gcms" folder (3 files)
• all files beginning with "tutogcms" in the "topics/metabolomics/images" folder (6 files)
• the CONTRIBUTORS.yaml file (addition of Julien as a contributor)

This corresponds to the following commits:

commit message	original commit id	rebased commit id
add gcms tuto	[1bef566]	[6be6743]
add new gcms	[5c1e761]	[f17d08a]
change bad ref	[0a37814]	[910e35c]
add doi and publi	[5a492f9]	[89a7ead]
Update topics/metabolomics/tutorials/gcms/tutorial.md	[0e2ce53]	[5556c9b]
Update topics/metabolomics/tutorials/gcms/tutorial.md	[598f4cc]	[89e9e70]

Are the details here enough?

[jsaintvanne]

Thank you @melpetera to continue my work ! I hope it helps and sorry to have not finish it during my time in Nantes !

Thank you also to all reviewers !

[hexylena]

Yes, that's great @melpetera I'll try and rebase everything.

[hexylena]

I pushed a branch with what is currently in this branch as a 'backup' in case we find out I did something wrong :) https://github.com/galaxyproject/training-material/compare/gtn_jsa_gcms-BACKUP

~But I think I've got the branch here corrected.~ soon

[hexylena]

Ok, for whatever reason I cannot push directly to your branch. I've tried and usually github handles that well, but, this time my commits to your branch are being rejected (or it's just creating a branch on the GTN repo. Weird.)

Could you run these commands @melpetera, it should fix the rebase.

If you don't know the name of the usptream remote, check it.

$ git remote -v | grep galaxyproject/training-material
upstream    git@github.com:galaxyproject/training-material.git (fetch)
upstream    git@github.com:galaxyproject/training-material.git (push)

If that's not there, add it

git remote add upstream git@github.com:galaxyproject/training-material.git

Now we'll get some copies of the commits that are relevant, to make sure they don't disappear

git checkout gtn_jsa_gcms
git format-patch e11be0c8c5b6dbca6d10292ae5387c3659260076 # This produces 12 files, we want 6 of them. I think it's because of rebase

And now reset the branch to the current upstream/main branch

git fetch upstream
git reset --hard upstream/main

And now we can re-add the commits. I think this selection of commits will produce the correct result

git am -3 0007-add-gcms-tuto.patch # This had a correction
git am -3 0002-add-new-gcms.patch
git am -3 0003-change-bad-ref.patch
git am -3 0004-add-doi-and-publi.patch
git am -3 0005-Update-topics-metabolomics-tutorials-gcms-tutorial.m.patch
git am -3 0006-Update-topics-metabolomics-tutorials-gcms-tutorial.m.patch

And now you can git push -f to overwrite the branch

[hexylena]

It looks good!! Thanks @melpetera

[melpetera]

Yeah! I did it!!!! 🎆

Thank you very much @hexylena for your time and the detailled procedure.

Thanks also @gallardoalba for your time, and also my colleague Nils for his supervision when I executed the procedure (I was so afraid to break everything by mistake, thank you for your psychological support!).

[melpetera]

May someone from @galaxyproject/training-metabolomics maybe review the PR? It is only an "enable:false" tutorial PR but I suppose I am not supposed to validate it myself now that I am more or less on-board this tutorial dev?

[gallardoalba]

May someone from @galaxyproject/training-metabolomics maybe review the PR? It is only an "enable:false" tutorial PR but I suppose I am not supposed to validate it myself now that I am more or less on-board this tutorial dev?

I'll have a look at it :)

[hexylena]

Thanks @melpetera @jsaintvanne @gallardoalba @yguitton for all the work getting this in!

[melpetera]

Thanks you very much to all of you!!! 🎆