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genomehubs / demo

Example configurations to set up custom Ensembl sites using GenomeHubs
genomehubs.org
MIT License
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demo fails to start #4

Closed ajs6f closed 6 years ago

ajs6f commented 6 years ago

Hi, I'm trying to set up a demo of GenomeHub as described here but startup is failing out with a problem finding a config file:

awk: cannot open /ensembl/conf/database.ini (No such file or directory)

Here's the whole log for review. I'm assuming that the awk calls are getting made inside some Dockerfile or setup script in one of the many images that are involved here?

Thanks for any help!

sujaikumar commented 6 years ago

Thanks for pasting the whole log. Yes, you're right - it's all happening inside the docker images. I'll have a look through and let you know if I get the same problem

sujaikumar commented 6 years ago

Just checking - did you do a git clone into your home directory?

The import.sh script makes the assumption that you were in ~ when you did git clone https://github.com/genomehubs/demo.git

That's why it tries to mount the docker folders to ~/demo/genomehubs-import/ensembl/conf in demo/import.sh line 30.

If you've git cloned into a different folder than ~/demo, just do a find and replace for ~/demo in import.sh.

Hope this helps

ajs6f commented 6 years ago

Yep. that seems to be it. With respect, that seems like a questionable assumption to me-- once this setup run completes (assuming successful completion) I'll send a PR for that.

sujaikumar commented 6 years ago

I agree. It was an assumption of convenience :-)