svg output seems broken

[hasindu2008]

Binaries on Linux were used.

command tried:

 /install/squigualiser-v0.6.3/squigualiser plot -f sampled_context_strands.fa -a f5c.bam -s control_rep1.blow5 --region rand_ref_RNA_01:30-70 -o plot1/ --rna --save_svg

Testset available here

Reported here hasindu2008/f5c#195 (comment).

I get a different issue when I try though:

Traceback (most recent call last):
  File "/install/squigualiser-v0.6.3/bin/squigualiser", line 8, in <module>
    sys.exit(main())
  File "/install/squigualiser-v0.6.3/lib/python3.8/site-packages/src/__init__.py", line 56, in main
    args.func(args)
  File "/install/squigualiser-v0.6.3/lib/python3.8/site-packages/src/plot.py", line 1079, in run
    export_svgs(layout_, filename=output_file_name)
  File "/install/squigualiser-v0.6.3/lib/python3.8/site-packages/bokeh/io/export.py", line 207, in export_svgs
    svgs = get_svgs(obj, width=width, height=height, driver=webdriver, timeout=timeout, state=state)
  File "/install/squigualiser-v0.6.3/lib/python3.8/site-packages/bokeh/io/export.py", line 293, in get_svgs
    web_driver = driver if driver is not None else webdriver_control.get()
  File "/install/squigualiser-v0.6.3/lib/python3.8/site-packages/bokeh/io/webdriver.py", line 138, in get
    self.current = self.create()
  File "/install/squigualiser-v0.6.3/lib/python3.8/site-packages/bokeh/io/webdriver.py", line 142, in create
    driver = self._create(kind)
  File "/install/squigualiser-v0.6.3/lib/python3.8/site-packages/bokeh/io/webdriver.py", line 160, in _create
    raise RuntimeError("Neither firefox and geckodriver nor a variant of chromium browser and " \
RuntimeError: Neither firefox and geckodriver nor a variant of chromium browser and chromedriver are available on system PATH. You can install the former with 'conda install -c conda-forge firefox geckodriver'.

[hiruna72]

Hey, where did you try this? It worked fine for me on gtgpu and gta100?

[hasindu2008]

It was on my laptop - WSL Ubuntu. Likely on those two servers a dependency is by default installed. Try on a minimal Ubuntu image.