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gamcil / clinker

Gene cluster comparison figure generator
MIT License
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Can't save changes to session #93

Closed camilo-monge closed 1 year ago

camilo-monge commented 1 year ago

Hello and thank you for your wonderful tool.

I have been using clinker for a while now, usually on the cagecat server. Since it has been down for the last weeks I've been trying to use it locally (installed in ubuntu via pip), however, I haven't been able to save/ reload any changes in my session.

I am running it as clinker *.gbff -p clinker.html -s session.json and everything works fine, but when I try to reload later with either clinker -p clinker.html -s session.json or clinker *.gbff -s session.json An error tells me that files are needed, and if I add them by running clinker *.gbff -p clinker.html -s session.json the program runs the alignments again and the changes made in my previous session are not reflected. I remember that the cagecat server had a " save session state" or similar which I cannot find in the local version. How can I save session state locally?

Thanks for the help.

gamcil commented 1 year ago

Hey @camilo-monge, thanks for the report. This is definitely a bug - clinker currently throws an error if no file paths are provided before it checks for a session file. I will fix this in the next release.

As for the session state, the visualisation part of clinker has a 'Save data' button for saving the state of the visualisation (configuration for the plot + plot data) which is different to the session file produced on the command line. That will allow you to save/load a visualisation directly in the browser. To open a blank clinker visualisation you can run clinker -p, then load your saved JSON with the 'Choose file' button in the right hand side menu.

camilo-monge commented 1 year ago

Hey @gamcil thanks for the guidance. Apparently the issues I was having were due to installing with pip, which gives ver 0.0.7, which does not allow to save session changes. I installed the conda version and works like a charm. Wonder why that happened, since I cloned just as explained in the github about two weeks ago.

Happy holidays!