GenomeHubs
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GenomeHubs
Introduction
Introduction
GenomeHubs
Files and containers
Demo
Quick Start
1. Prepare
2. Setup MySQL database server
(optional) Test Ensembl browser
3. Import assembly and gene models
4. Export files
5. Run analyses
6. Import analysis results
7. Update meta
8. Start download site
9. Start BLAST server
10. Start search container
11. Edit Ensembl plugin
12. Start Ensembl browser
Next Steps
Setup with multiple hosts
Understand the GFF parser
Import additional assemblies
Run comparative analyses
Import variation data
Add track hubs
Connect using Perl API
Set up REST API
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8. Start download site
GenomeHubs provides an h5ai container to host files for download. Any files in directories mounted in the container under /var/www/html will be available for download so additional files can be hosted alongside the files generated in previous steps.

Edit files in conf directory

Edit Masthead.html to change the site name, logos and link urls:
  • add images to the ~/genomehubs/v1/download/conf/img directory if you wish to include them on your site
  • further changes to the appearance can be made by editing the styles in custom.css
$ cd ~/genomehubs/v1/download/conf
$ nano Masthead.html
# replace references to example.com with your domain name
Edit _h5ai.headers.html to change the message that will be printed at the top of all directory listings:
$ nano _h5ai.headers.html
# replace with your own message

Start h5ai downloads container

Start the h5ai Docker container:
$ docker run -d \
--name genomehubs-download \
-v ~/genomehubs/v1/download/conf:/conf:ro \
-v ~/genomehubs/v1/download/data:/var/www/html/v1:ro \
-p 8882:8080 \
genomehubs/h5ai:19.05
Quick Start - Previous
7. Update meta
Next - Quick Start
9. Start BLAST server
Last modified 2yr ago
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Outline
Edit files in conf directory
Start h5ai downloads container