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genomehubs / demo

Example configurations to set up custom Ensembl sites using GenomeHubs
genomehubs.org
MIT License
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issues setting up the DEMO on a HEADLESS server #7

Open M3hran opened 6 years ago

M3hran commented 6 years ago

I have ran into issues running the demo site on an VM as a demo for Smithsonian Inst.

I have changed the following parameters inside /gh-ensembl-plugin/conf/ini-files/DEFAULTS.ini to get around the local loopback issues (127.0.0.1) 

BLAST_URL = http://0.0.0.0:8083
DOWNLOAD_URL = http://0.0.0.0:8082
ASSEMBLY_STATS_URL = http://0.0.0.0:8082/html/assembly-stats/assembly-stats.html?path=/demo/json/assemblies/&
CODON_USAGE_URL = http://0.0.0.0:8082/html/codon-usage/codon-usage.html?path=/demo/json/annotations/&

The main ensembl site comes up on my public IP on port 8081 and i'm able to browse each "modules" on 8082,and 8083 individually. However the main site on 8081, shows broken links (404) when clicking on "Blast" or "BioMart", not sure if other links are working correctly either.

access logs on the container, show: [444/- - -/-=-] 160.111.254.17/- -/- -/- [17/Oct/2017:19:54:29 +0000] "GET /Multi/Tools/Blast?db=core HTTP/1.1" 404 3222 "http://34.193.222.50:8081/index.html" "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/61.0.3163.100 Safari/537.36" "-" -/-

rjchallis commented 6 years ago

Thanks for this suggestion. Using 0.0.0.0 as the default for the plugin seems more sensible than defaulting to 127.0.0.1 so I've updated this in gh-ensembl-plugin.

Ensembl BLAST and BioMart won't work in the demo. With the GenomeHubs plugin, BLAST links should all go to SequenceServer (port 8083). BioMart is not currently supported (and I wasn't aware that the links were still available). Where on the site were the BLAST and BioMart links? It seems like it could be a case of the plugin not loading correctly.

M3hran commented 6 years ago

The links appear in the main menu of index.html , the first item is "BLAST" the second is "BioMart" then, "Tools", Downloads", "Dcoumentation", and "Website Help".

:8081/Multi/Tools/Blast?db=core :8081/biomart/martview

rjchallis commented 6 years ago

Sounds like your site is running with the Ensembl Metazoa plugin - this shouldn't happen with the demo script but digging around I hadn't realised that the old README files are still in the various subdirectories.

If you are following one of these then either the basic-mirror (which only gets as far as an unskinned Ensembl Metazoa mirror) or the genomehubs-mirror (which has a step in the middle that has the basic site before further steps to get to a GenomeHubs site) README files would get you to a site with broken menus as more steps are needed before all the data are in place for the gh-ensembl-plugin.

I made the demo script for the publication and forgot that the step-by-step instructions were still there so I haven't updated them in line with the newer documentation, etc. So I certainly need to update these but given that you made changes to gh-ensembl-plugin to get around local loopback issues, I'm not certain that this is what is causing these links to show up.

Could you confirm if you are running the demo.sh/import,sh scripts or following the step-by-step instructions so I know what to try and fix.