igv_plotter --genome ref.fa readsSorted.bam --locus-file locus_file.txt --max-memory 10G Traceback (most recent call last): File "/Users/user/anaconda/envs/python3env/bin/igv_plotter", line 140, in <module> igv_robot.execute() File "/Users/user/anaconda/envs/python3env/lib/python3.6/site-packages/igv_api.py", line 256, in execute self._execute_impl(self.__command_queue) File "/Users/user/anaconda/envs/python3env/lib/python3.6/site-packages/igv_api.py", line 387, in _execute_impl fake_display.start() File "/Users/user/anaconda/envs/python3env/lib/python3.6/site-packages/xvfbwrapper.py", line 79, in start raise RuntimeError('Xvfb did not start') RuntimeError: Xvfb did not start
locus_file.txt only contains this:
I:10,000-20,000. From reading online, it seems that this Xvfb is what I need to be able to use IGV without a GUI. I am working on Mac High Sierra and I don't know if I can install Xvfb on Mac OS X or how I can do it. I was quickly out of my depths on the online posts about Xvfb on Mac. I checked that I installed igv_plotter correctly by successfully pulling out the help with
igv_plotter -h. I could not find Xvfb using brew.
Opening IGV and making a screenshot is not a viable option for me, as I would like to export hundreds or thousands or regions.