Move tools from sub repos

[bernt-matthias]

I'm currently trying to get rid of the last conda environments on my instance, i.e. all that do not yet have a biocontainer. Quiet a few of them are from https://github.com/workflow4metabolomics/ (all those which are not yet in https://github.com/workflow4metabolomics/tools-metabolomics).

With the help of @bgruening I will try to manually construct containers for the current versions. In order to make this sustainable we can either:

1. add IUC style CI to all the subrepos and add them to the planemo-monitor
2. move the tools to the main repo, would require access to the corresponding toolshed accounts to provide admin access to the TS repos for the user used in the main repo.
3. another solution would be to deprecate these tools, which should be done in the TS and github

Main motivation is to get maintenance (i.e. transfer them to the community maintained repo) for these tools (if still needed).

What do you all think? Ping @yguitton @lecorguille @fgiacomoni @ethevenot @melpetera @marie-tremblay-metatoul @mmonsoor.

The preference of @hechth and myself would be to move the tools (or deprecate if the tool is not of any use anymore).

I will collect tools sorted by owner and some infos below here (the list might grow):

• eschen42/w4mkmeans = https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper
• eschen42/w4mclstrpeakpics = https://github.com/HegemanLab/w4mclstrpeakpics_galaxy_wrapper
• ethevenot/biosigner = https://github.com/workflow4metabolomics/biosigner
• ethevenot/multivariate/ = https://github.com/workflow4metabolomics/multivariate
• ethevenot/profia = https://github.com/workflow4metabolomics/profia
• ethevenot/qualitymetrics/ = https://github.com/workflow4metabolomics/qualitymetrics
• ethevenot/univariate = https://github.com/workflow4metabolomics/univariate
• fgiacomoni/bank_inhouse = ???
• fgiacomoni/golm_ws_lib_search = https://github.com/workflow4metabolomics/tool-bank-golm-lib_search
  • seems broken due to API change
• fgiacomoni/hmdb_ms_search/ = https://github.com/workflow4metabolomics/tool-bank-hmdb
  • tool broken (URL endpoint fails)
• fgiacomoni/lipidmaps_textsearch = https://github.com/workflow4metabolomics/tool-bank-lipidMaps
  • tool seem broken (API changed)
• fgiacomoni/massbank_ws_searchspectrum = https://github.com/workflow4metabolomics/wrapper-bank-massbank-spectrum_search
  • tool seems broken since API changed? Is this a good replacement?
• lecorguille/anova/abims_anova= https://github.com/workflow4metabolomics/anova
• marie-tremblay-metatoul/nmr_bucketing = https://github.com/workflow4metabolomics/nmr_bucketing
• marie-tremblay-metatoul/asca = https://github.com/workflow4metabolomics/ascaw4m
• melpetera/batchcorrection/ = https://github.com/workflow4metabolomics/batch_correction
• melpetera/corr_table = https://unh-pfem-gitlab.ara.inrae.fr/pfem-public/tool-correlationtable
• mmonsoor/probmetab = https://github.com/workflow4metabolomics/probmetab
• prog/lcmsmatching/ -> https://github.com/workflow4metabolomics/lcmsmatching

[melpetera]

Dear @bernt-matthias @bgruening and @hechth

Thank you for this complete listing and reviewing. Truth is we discussed this question last december in a W4M coreteam meeting. To make a little history, we aggreed a few years ago to go for the option '2' you mentioned. Unfortunately, as months and years have gone by, alsmost nothing happend, since we decided to handle it tool by tool at each maintainer's pace, which sadly led to never put it on the top of the list. As this issue became critical, we decided last december to plan a dedicated hackathon to handle it for good this time, but we have not yet settled the date (truth is we were supposed to settle the day today, but it got delayed).

So now the question is: will our W4M hackathon timeline match your needs, or do we need to adjust a plan for quicker action? Do you have any deadline or need for all this to be ready before? To note, I doubt we will be able to schedule our W4M hackathon before April from my "multi-sites planning experience", with I think a probable date arround June 2025. But we can maybe settle a compromise that can be quickly deployed to cope with the delay between now and the hackathon, if needed.

[melpetera]

To note: the tool here: https://toolshed.g2.bx.psu.edu/repos/melpetera/corr_table
has its code here: https://unh-pfem-gitlab.ara.inrae.fr/pfem-public/tool-correlationtable

Ideally to also move to tools-metabolomics.

[bernt-matthias]

we decided last december to plan a dedicated hackathon to handle it

Great idea.

So now the question is: will our W4M hackathon timeline match your needs, or do we need to adjust a plan for quicker action?

The hackathon is perfect. The main motivation for this issue was to keep track. For the W4M tools installed on my server (I guess its a large fraction) we made a bit of progress to provide containers for the current versions: BioContainers/multi-package-containers#3411

[bernt-matthias]

I guess another great goal would be to have the W4M workflows in https://github.com/galaxyproject/iwc