GitHub Actions for MMT (Metabolite version of GMT)

[kozo2]

https://github.com/kozo2/AHWikipathwaysDbs/blob/main/inst/scripts/make-data.R
does it in the Bioconductor's AnnotationHub framework,
but it should be done in the GitHub Actions (of this repo).

[kozo2]

@AlexanderPico
Is it possible to download meta-data-action-1.1.1-jar-with-dependencies.jar from somewhere?
I have come to think that with a datanode file I may not need MMT.
So I would like to try meta-data-action-1.1.1-jar-with-dependencies.jar locally.

[larsgw]

I believe it is here: https://github.com/wikipathways/meta-data-action/blob/main/meta-data-action-1.1.2-jar-with-dependencies.jar

[kozo2]

@larsgw , thank you for the information 🙏
By the way, do you know how to use this jar file from command line?
I tried the following command, but it seems that the --help or -h options don't explain this.

PS C:\Users\kozo2\Downloads> java -jar .\meta-data-action-1.1.2-jar-with-dependencies.jar
Wrong number of attributes
PS C:\Users\kozo2\Downloads> java -jar .\meta-data-action-1.1.2-jar-with-dependencies.jar --help
Wrong number of attributes
PS C:\Users\kozo2\Downloads> java -jar .\meta-data-action-1.1.2-jar-with-dependencies.jar -h
Wrong number of attributes

[kozo2]

@larsgw I'm sorry 🙇 I found it.
The command-line options were written in https://github.com/wikipathways/meta-data-action?tab=readme-ov-file#using-the-metadataextractor-locally .
If I can obtain the data I need with these options, I will close this issue.