IGV-snapshot-automator
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invalid literal for int() with base 10 error
Hi,
First of all, thank you for this script-based IGV visualization.
When I run your demo dataset and also mine, I obtained error that I attached it as screenshot below:
Can I solve this issue?
Thanks for your interest.
Best wishes.
You might try commenting out these two lines;
https://github.com/stevekm/IGV-snapshot-automator/blob/d2c01a5d683ce29ba7c0a8920f563b467f924d32/make_IGV_snapshots.py#L223-L224
I had previously been using this method to obtain an open xvfb server number;
https://github.com/stevekm/IGV-snapshot-automator/blob/d2c01a5d683ce29ba7c0a8920f563b467f924d32/make_IGV_snapshots.py#L120-L135
However I later found that many systems include xvfb-run --auto-servernum
method which I switched over to using here;
https://github.com/stevekm/IGV-snapshot-automator/blob/d2c01a5d683ce29ba7c0a8920f563b467f924d32/make_IGV_snapshots.py#L227
however the original call to xdpyinfo
is still present and it appears that the version on your system is giving a different response than expected.
If commenting out that works for you I can make a fix in the script for it as well. Thanks.
this whole process is a little tricky since it seems like different systems have slightly different versions of xdpyinfo
and xvfb-run
which can cause problems like this.
marking this as a bug that I should probably fix; just get rid of the old command that is not needed anymore