Complete Documentation

[ttbek]

Several areas of cloudgene.io have incomplete documentation, e.g. http://docs.cloudgene.io/daemon/administration/

I can't find anything about how to modify the webui other than that it uses some combination of javascript, java, and is built with nodejs grunt and maven. It is really very unclear to me still though.

I found this https://scotch.io/tutorials/use-ejs-to-template-your-node-application

Which suggests to me that placing .ejs files in /data/pages (based on the cloudgene.conf file) would be used to replace the defaults? That doesn't seem to work for me though. Does it need to be totally rebuilt, ala the DEVELOPING.md file?

I may just be in over my head with this framework.

[ttbek]

Ah, with the right permissions it seems to work for say home.ejs, but not for say help.ejs, which I was trying when I opened the issue, it continues to link to the github page instead. I guess to make other changes I will need to modify the index.html or will I need to rebuild?
For instance, to change the line:"powered by Cloudgene and supported by the U.S. National Institutes of Health and the FWF Austrian Science Fund" to "powered by Cloudgene" as our work is not supported by the NIH or FWF Austrian Science Fund.

[lukfor]

Documentation is currently work in progress. Cloudgene has some mechanisms to integrate pages (like help.ejs) without rebuilding the webapp using grunt. Unfortunately, this feature is not yet documented :( I keep you updated as soon as a tutorial is ready!

[ttbek]

I figured out how to point the help page elsewhere and change the appname, they are set in the settings.yaml

Snippets:

navigation: !java.util.Vector
- !cloudgene.mapred.util.MenuItem
id: help
name: Help
link: HELP_LINK_URL_GOES_HERE

and the name that appears in the upper left of every page:

name: NAME_GOES_HERE

I suppose these will be added to this section of the documentation later: http://docs.cloudgene.io/daemon/configuration/ Though the settings.yaml doesn't seem to be exclusive to running the daemonized version.

Still not sure about removing "powered by Cloudgene and supported by the U.S. National Institutes of Health and the FWF Austrian Science Fund" to "powered by Cloudgene," I don't want it to be misconstrued that NIH or FWF are endorsing us.

[lukfor]

At the moment, the footer message is stored in the database.
You can change it in the Admin Panel by clicking on Templates. There is a key FOOTER which contains the footer message.

I am working hard on updating the documentation ;)