Tool request: MZMine - Githubissues

workflow4metabolomics / tools-metabolomics

Galaxy tools for metabolomics maintained by Workflow4Metabolomics

https://workflow4metabolomics.org/

GNU General Public License v3.0

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Tool request: MZMine #240

Closed bernt-matthias closed 1 year ago

bernt-matthias commented 1 year ago

I will work on mzMIne .. help welcome

[ ] bioconda https://github.com/bioconda/bioconda-recipes/pull/40700
- [ ] check if its possible to run GUI via container ($DISPLAY?)
- [x] use --help and/or --version for tests https://github.com/bioconda/bioconda-recipes/pull/40700/commits/3ab75b20b1a597cf8f09128f217fec116eb070b5
- [x] finish after new mzMine release https://github.com/bioconda/bioconda-recipes/pull/40700/commits/3ab75b20b1a597cf8f09128f217fec116eb070b5
[ ] tool for batch processing
- inputs
- mzml files (as symlinks in input dir)
- optional: annotation (csv), spectral library (user supplied / central reference data)
- outputs
- mgf file(s)
- csv file(s)
- future: mzMine project
- set threads and tmp dir via config file (maybe in the future CLI parameter)
- batch processing mode (input mzmine xml file(s))
[ ] tool that creates and processes mzmine xml files

yguitton commented 1 year ago

Hi @bernt-matthias

Really go idea, I'm not a docker expert, but maybe @Lain-inrae or @lecorguille can help at some point depending on your needs. It would be really cool to have mzMine batch processing implemented

Best Yann

bernt-matthias commented 1 year ago

Wonderful. We may speed up development by starting tool development using a container. If I understood the mzmine developers right there should be one available (or at least easy to build one). We can switch to bioconda/biocontainers as soon as the mzmine bioconda recipe works.

bernt-matthias commented 1 year ago

I would like to have a VC on Tuesday (June 20th) with Robin Schmid. 10:00 or 13:00 CET (ie Berlin time) would work for both of us. Do you have any preferences regarding the time? Would be cool if some of you could join.

Ping @yguitton @Lain-inrae @lecorguille @chufz ..

hechth commented 1 year ago

@bernt-matthias I'd jump in if you don't mind - 1pm is preferred for me but can also make 10am.

bernt-matthias commented 1 year ago

Then lets make it 1pm. Anyone else: just ping me and I send you the VC details per mail.

chufz commented 1 year ago

I am also free 1pm and happy to join.

yguitton commented 1 year ago

Hi, sorry not available, but if possible keep me updated

Best

bernt-matthias commented 1 year ago

Hi there. 1st version over here: https://github.com/workflow4metabolomics/tools-metabolomics/pull/241

Suggestions (in particular) if we could/should split output in multiple collections (or just use simple datasets). Problem is that we do not know what kind of outputs are configured in the output.

We could define single dataset outputs for each possible output type (and add another select box allowing the user to choose [again] what is needed)
dynamically discovered outputs
A small set of collections that contain related outputs

I think 2 would not work in Galaxy workflows.

bernt-matthias commented 1 year ago

Bioconda recipe is ready in my opinion.

bernt-matthias commented 1 year ago

I'm pushing this to IUC. Seems that the W4M repo is on hiatus at the moment.