JMRUI in the command line

[Amber Howell]

Hi! I posted in another section asking about running JMRUI through the command line, since batch processing wasn’t working. I was given three new .jar files (for zerofilling, apodizing, and hard-phasing) that fixed this issue in windows.
However, after swapping out this jar files, I’m getting an error where JMRUI freezes after processing. When running through the command line, I see that the steps I wanted are labelled as “Done!”, but the program doesn’t quit. I need to press control+C and exit batch mode to run a new command line. In the GUI, once processing is done and I save the file, the gui freezes and I need to restart JMRUI.

I also swapped the jar files while running JMRUI on linux (jmrui.sh). Now the JMRUI gui won’t let me manually change things (like zerofill or any other processing steps). It lets me click the tabs and buttons, but nothing happens to the data (and the little boxes don’t pop up – like being able to add the number of zeros I want to add in zero fill). I also still cannot run it through the command line.

I think if these two bugs were to be fixed (being able to run multiple commands through the command line without having to copy/paste them individually after exiting batch mode) and then being able to do these same things on the linux server, batch processing in JMRUI would be very smooth.

Lastly, this isn’t a bug, but JMRUI automatically outputs your files as .mrui files in batch mode, but in the gui you can click (save as > .mrui) and then change .mrui to .txt when the file browser window pops up. Is there a way to save these files as .txts when running JMRUI through the command line? Or if you have a suggestion for how to convert the .mrui -> .txt files after processing in some sort of automated way (right now I have to open each .mrui and manually save it as a .txt) that would be absolutely fantastic.

Thank you so much!

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