vreuter
commented
3 months ago May additionally or alternatively want xvfb: https://packages.ubuntu.com/jammy/xvfb
Closed vreuter closed 3 months ago
vreuter
commented
3 months ago May additionally or alternatively want xvfb: https://packages.ubuntu.com/jammy/xvfb
vreuter
commented
3 months ago Indeed, we do....
Traceback (most recent call last): │········
File "/opt/conda/lib/python3.10/site-packages/napari/window.py", line 14, in <module> │········
from napari._qt import Window │········
File "/opt/conda/lib/python3.10/site-packages/napari/_qt/__init__.py", line 77, in <module> │········
from napari._qt.qt_event_loop import get_app, gui_qt, quit_app, run │········
File "/opt/conda/lib/python3.10/site-packages/napari/_qt/qt_event_loop.py", line 11, in <module> │········
from qtpy.QtGui import QIcon │········
File "/opt/conda/lib/python3.10/site-packages/qtpy/QtGui.py", line 57, in <module> │········
from PyQt6 import QtGui │········
ImportError: libEGL.so.1: cannot open shared object file: No such file or directory │········
│········
The above exception was the direct cause of the following exception: │········
│········
Traceback (most recent call last): │········
File "/looptrace/bin/cli/run_processing_pipeline.py", line 328, in <module> │········
main(sys.argv[1:]) │········
File "/looptrace/bin/cli/run_processing_pipeline.py", line 323, in main │········
pipeline.run(start_point=opts.start_point, stop_after=opts.stop_after) │········
File "/opt/conda/lib/python3.10/site-packages/pypiper/pipeline.py", line 319, in run │········
stage.run() │········
File "/opt/conda/lib/python3.10/site-packages/pypiper/stage.py", line 56, in run │········
self(*args, **kwargs) │········
File "/opt/conda/lib/python3.10/site-packages/pypiper/stage.py", line 64, in __call__ │········
self.f(*args, **kwargs) │········
File "/looptrace/bin/cli/nuc_label_qc.py", line 101, in workflow │········
save_screenshot(viewer=viewer, outfile=outfile) │········
File "/opt/conda/lib/python3.10/site-packages/looptrace/napari_helpers.py", line 92, in save_screenshot │········
screenshot = add_screenshot(viewer, flash=flash, **kwargs) │········
File "/opt/conda/lib/python3.10/site-packages/looptrace/napari_helpers.py", line 78, in add_screenshot │········
screenshot = viewer.screenshot(flash=flash, **kwargs) │········
File "/opt/conda/lib/python3.10/site-packages/napari/viewer.py", line 129, in screenshot │········
return self.window.screenshot( │········
File "/opt/conda/lib/python3.10/site-packages/napari/window.py", line 27, in __getattr__ │········
raise type(err)( │········
ImportError: An error occured when importing Qt dependencies. Cannot show napari window. See cause above │········napari is being removed from the pipeline, and visualisation handled separately
https://napari.org/stable/howtos/headless.html