Quite new to NGSEP and the world of bioinformatics. Trying to run NGSEP GUI on linux (ubuntu 22.04 [Jammy Jellyfish]) and have continuously run into an issue whenever NGSEP's trying to open up another window of files (i.e. clicking 'Explorer' in an attempt to change root folder or when trying to browse for an input file; see attached files)
Thanks for your interest in NGSEP. The current GUI has been tested in Ubuntu 20 running java 11. It is not easy for me to test with Ubuntu 22 at this time, but I could test with Ubuntu 23. Although I did not get the same error, the behavior of the file explorer was also weird. In all operative systems, these errors are normally related to the version of JavaFX, which is the infrastructure behind the graphical interface. By default we are including in the package a rather old version of javaFX (version 11), which now I see that it is not working on newer systems. To solve the issue, I just updated the version of JavaFX to the latest version with long term support (21.0.1). To make this update, please follow these instructions:
Download the latest LTS SDK version of java FX from this link (https://gluonhq.com/products/javafx/)
Extract the contents of the tar.gz file within the folder NGSEPlinux (where the run.sh is located). The folder javafx-sdk-21.0.1 should appear within the directory NGSEPlinux along with the folder javafx-sdk-11.0.2, which was included in the NGSEP package.
Edit the file "run.sh" to modify the folder where the javaFX files are located. Replace "javafx-sdk-11.0.2/lib" with "javafx-sdk-21.0.1/lib".
Start NGSEP running the script "run.sh" from the command line.
Because version 21 of JavaFX was just released, it may not work fine with Ubuntu 22. If that does happen, you can try the previous LTS version (17.0.9). In any case, let me know how things go.
Best regards
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Anonymous
Anonymous
-
2023-10-24
Hi Jorge,
Thank you so much for your program and for your quick support
I tried using both 21.0.1 version and 17.0.9. Editing the java version to 21.0.1, running rush.sh does not open anything at all. Using 17.0.9 does open NGSEP, but unfortunately leads to the same initial GUI error when clicking explore :(
Best wishes
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Sorry to hear this. We will try to reproduce the error in an ubuntu 22 and get back to you. In the mean time, for the experiment with version 22.0.1, if possible please share the edited run.sh, a screenshot of the NGSEPlinux folder and the message that you get (if any) when running the run.sh script from the command line.
Best regards
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello,
Quite new to NGSEP and the world of bioinformatics. Trying to run NGSEP GUI on linux (ubuntu 22.04 [Jammy Jellyfish]) and have continuously run into an issue whenever NGSEP's trying to open up another window of files (i.e. clicking 'Explorer' in an attempt to change root folder or when trying to browse for an input file; see attached files)
Any help would be greatly appreciated thank you!
Thanks for your interest in NGSEP. The current GUI has been tested in Ubuntu 20 running java 11. It is not easy for me to test with Ubuntu 22 at this time, but I could test with Ubuntu 23. Although I did not get the same error, the behavior of the file explorer was also weird. In all operative systems, these errors are normally related to the version of JavaFX, which is the infrastructure behind the graphical interface. By default we are including in the package a rather old version of javaFX (version 11), which now I see that it is not working on newer systems. To solve the issue, I just updated the version of JavaFX to the latest version with long term support (21.0.1). To make this update, please follow these instructions:
Because version 21 of JavaFX was just released, it may not work fine with Ubuntu 22. If that does happen, you can try the previous LTS version (17.0.9). In any case, let me know how things go.
Best regards
Hi Jorge,
Thank you so much for your program and for your quick support
I tried using both 21.0.1 version and 17.0.9. Editing the java version to 21.0.1, running rush.sh does not open anything at all. Using 17.0.9 does open NGSEP, but unfortunately leads to the same initial GUI error when clicking explore :(
Best wishes
Sorry to hear this. We will try to reproduce the error in an ubuntu 22 and get back to you. In the mean time, for the experiment with version 22.0.1, if possible please share the edited run.sh, a screenshot of the NGSEPlinux folder and the message that you get (if any) when running the run.sh script from the command line.
Best regards