PRONTO version 1.0

[xiaoliz0]

This is PRONTO release version 1.0

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This discussion was created from the release PRONTO version 1.0.

[xiaoliz0]

This is PRONTO release version 1.0. Please write your feedback, comments, bug reports, suggestions here. We could discuss and make a requests list for the next version updates.

[marrip]

667 MB is no problem for docker hub (not the same as github), we could even set up a CI integration via gitlab actions if you want. I think it would be good to publish all inpred related images under the inpred account there so that people can easily access them :)

[tinavisnovska]

having the images shared via docker hub would be great, in principle singularity images should be pull-able from there without any extra work on the developers side. However, we should be careful not to make any proprietary data accessible by accident,...

[marrip]

agreed, one should be cautious with proprietary data. I guess anything is published on GitHub it should already be checked for that - if we build directly from GitHub it might be even safer than pushing locally build images 👍

[xiaoliz0]

Okay. Docker hub sounds a good place to put the image. I will check it. :)

[marrip]

this project is doing an automatic build and push to the registry at docker hub: https://github.com/InPreD/local_app_prepper/tree/develop
and here is the repo at docker hub:
https://hub.docker.com/repository/docker/inpred/local_app_prepper/general

[xiaoliz0]

1. Upload docker image to the InPreD Docker Hub.

[marrip]

I see you added the actions! Looking good 🎉

[xiaoliz0]

Thank you for your help Martin! It worked after some failure attempts. I will test the image and update the documentation file for it. :)

[xiaoliz0]

Done. Put the Dockerfile in the InPreD/PRONTO repository and remove the PRONTO_image folder.

[xiaoliz0]

2. CNV_overview_plots file is missing in the Testing_data folder for CL_NA12878N25.

[xiaoliz0]

Done

[xiaoliz0]

3. Image scripts read the data_path of TSOPPI from the Config/configure_PRONTO.ini file.

[xiaoliz0]

Done. The data_path will be given by docker command when run PRONTO with image. Look the README page for docker commands.

[xiaoliz0]

4. PROTO will not update the InPreD_PRONTO_metadata_tsoppi.txt file if it does not exist in the folder Out/. Print a warning message not crash.

[xiaoliz0]

Done.

[tinavisnovska]

It would be great to have the possibility to define a ppt template as a parameter of PRONTO.py script. Especially handy in situations when alternative ppt template than the default one needs to be used - like when for example the year changes and we have a need to modify the template even though want to keep the old one at hand being able to use it. Another uscase (in our case at least) are reports generated within precision medicine activities which are not included into InPreD.

[tinavisnovska]

If not now, then for the future it would be great to have ChangeLog public.

[xiaoliz0]

5. PRONTO should give a warning message when the RNA smaple ID is missing in the meta file but existing int the SOPPI results. Still generate the report without sample material ID of RNA.

[xiaoliz0]

Done.

[xiaoliz0]

6. Update with new Overview of Nomenclature and upload the file to GitHub.

[xiaoliz0]

Done. Under Log/

[xiaoliz0]

7. New PP template with some sentences changes.

[xiaoliz0]

Done.

[xiaoliz0]

8. Summary changes document from Tonje to GitHub.

[xiaoliz0]

Done. Under Log/