Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Script does not run in headless mode #9

Open
hdeluna opened this issue Feb 14, 2019 · 1 comment
Open

Script does not run in headless mode #9

hdeluna opened this issue Feb 14, 2019 · 1 comment

Comments

@hdeluna
Copy link

hdeluna commented Feb 14, 2019

Hi, I just started using ImageJ and Docker a little ago, I'm trying to run a script, but an error keeps popping up. This is my command

sudo docker run -it --rm fiji/fiji fiji-linux64 --headless --run /path/to/script.txt 'file=/path/to/image/IMG_8919.JPG output_path=/path'

I also have the same file saved as a macro but the same error pops for both:

java.lang.IllegalArgumentException: Could not handle HTTPS in public boolean install(java.lang.String path) in ij.plugin.PluginInstaller
at net.imagej.patcher.CodeHacker.handleHTTPS(CodeHacker.java:1221)
at net.imagej.patcher.LegacyExtensions.injectHooks(LegacyExtensions.java:286)
at net.imagej.patcher.LegacyInjector.inject(LegacyInjector.java:308)
at net.imagej.patcher.LegacyInjector.injectHooks(LegacyInjector.java:109)
at net.imagej.patcher.LegacyEnvironment.initialize(LegacyEnvironment.java:101)
at net.imagej.patcher.LegacyEnvironment.applyPatches(LegacyEnvironment.java:495)
at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:397)
at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:376)
at fiji.IJ1Patcher.run(IJ1Patcher.java:37)
at net.imagej.launcher.ClassLauncher.patchIJ1(ClassLauncher.java:195)
at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:154)
at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
Feb 14, 2019 2:49:43 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
Unrecognized command: "/path/to/script.txt"
[ERROR] Skipping unsupported option -port7

What could be causing this and how could I solve it?

Thank you :)

@ctrueden
Copy link
Member

@hdeluna Sorry, this repository is not fully maintained right now. The person who created it left the project, and I don't really know much about how it works, so I cannot really support it. Pull requests are very welcome if you figure it out, though. At some point I do expect to dive into Docker more and update this repository, but do not have time in the near future.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants