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DennisSchmitz / Jovian_archive

Metagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail. Jovian aims to empower classical biologists and wet-lab personnel to do metagenomics/viromics analyses themselves, without bioinformatics expertise.
GNU Affero General Public License v3.0
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IGV can't access the data resources when using WSL #151

Closed florianzwagemaker closed 4 years ago

florianzwagemaker commented 4 years ago

It appears that the IGVjs html page we generate in the pipeline doesn't really work all that great on WSL-systems.

To be clear, the HTML-page itself works. But for the datastreaming we currently use the system hostname.

For WSL, this is a problem. The hostname is apparently translated to "localhost" (127.0.0.1) in a way that WSL can't reach it and/or WSL can't use it without changing settings in Windows.

Using the IP-address directly in the URL of our data-sources, instead of the hostname, solves this. The localhost-IP (127.0.0.1) can be used by WSL without problem.

Right now, i'll add this issue pretty low to our priority-list as the solution is relatively easy. (change the Hostname to the localhost-IP for the URLs in the file igv.html )

florianzwagemaker commented 4 years ago

This should be solved in the upcoming release (https://github.com/DennisSchmitz/Jovian/commit/d038008478953ff2e4cca50b4cad28114490c178)

Instead of using the hostname for all of our network-related scripts we will now use the local-network IP address of the computer.

This also makes the Jupyter notebook instance easier to use in a multi-server environment within a local network. i.e. you wish to run your analysis on server A, the Jupyter instance runs on server B, and you wish to view the results on computer C.

Using Jupyter notebooks over the public internet does not work with this method.