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g2nb / igv-jupyter

Extension for Jupyter which integrates igv.js
MIT License
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Trouble loading azure or local crams #51

Open kateelliottarc opened 8 months ago

kateelliottarc commented 8 months ago

Hi,

Many thanks for developing this.

I'm relatively new to azure and jupyter notebook, but have been able to set up and run igv-jupyter using the test run provided. The script starts the browser, finds your s3 aws file and produces a pileup.

However, with my data I'm hitting problems with trying to get the script to pick up and load my files. They are cram files are azure and I tried pointing to the url provided by azure for the files of interest, but get "Error accessing resource [url] Status: 0". I get the same even if if I try adding an SAS token, but that didn't help.

Next I tried copying the files to the local cloud machine and got a new error that only gives "408" in the dialog box and no error message.

Any help gratefully received.

Kate

jrobinso commented 8 months ago

Hi Kate. First are you using g2nb, or just igv-jupyter stand alone?

The URL error might be a CORS error (Cross Origin Resource Scripting) if the web host for the notebook is not the host you are fetching data from. Look for CORS errors in the javascript console. This is common and easily fixed by configuring the server to add CORS headers. I do not know how this is done for Azure but there is some general information here: https://github.com/igvteam/igv.js/wiki/Data-Server-Requirements. Also, do a web search for "CORS javascript" for more info.