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stevekm / IGV-snapshot-automator

Script to automatically create and run IGV snapshot batchscripts
GNU General Public License v3.0
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invalid literal for int() with base 10 error #21

Open kaanokay opened 3 years ago

kaanokay commented 3 years ago

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:

Screenshot from 2021-03-06 15-02-06

Can I solve this issue?

Thanks for your interest.

Best wishes.

stevekm commented 3 years ago

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.

stevekm commented 3 years ago

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.

stevekm commented 3 years ago

marking this as a bug that I should probably fix; just get rid of the old command that is not needed anymore