This is the first public release of the GenoRing project. It is in an alpha stage, meaning many features are missing and it contains bugs. It should be used with caution just to test things. How to proceed:
# git clone https://github.com/SouthGreenPlatform/genoring.git# cd genoring- Optional:
# git checkout tags/1.0.0-alpha6 # ./genoring.pl start- agree to the license
- it builds local GenoRing Docker container image (takes several minutes, 5-10min, maybe more depending on the computer)
- it asks environment questions:
- keep "dev"
- keep empty user ID (to keep current user)
- keep empty group ID (to keep current group)
- keep "genoring" admin name (or change it)
- set your own password
- set admin account email to your email (to get mail notifications)
- set site email to your email (or another one users can contact)
- keep or set site name
- set the "Drupal host" (server name) to your server IP or machine name if it can be resolved by the DNS
- keep trusted host pattern
- keep auto-update off
- validate GenoRing container settings
- keep database name
- keep database username
- set database password
- validate database settings
- GenoRing installs and pre-configures the system. You can ignore "ERROR" messages on the database logs.
- The site should be up and running on port 8080 (by default).
Go to your favorite web browser and access the site as displayed in the end of the installation:
http://<your_server_ip_or_name>:8080/
- You can connect as admin on the site, go back to the front page, and from there to the GenoRing dashboard (route:
/genoring/). - add a new "Genome Assembly"
- name it "Pahang" and fill metadata at your will except for "Data-related taxonomy" that should contain "Musa acuminata" (you can type "MUSAC" and select the auto-complete)
- FASTA data source: provide a file URI/URL and enter:
https://www.genoring.net/sites/default/files/samples/pahang/Musa_acuminata_pahang_v4.fasta
For metadata, same as above (with "MUSAC") - GFF3 data source: provide a file URI/URL and enter:
https://www.genoring.net/sites/default/files/samples/pahang/Musa_acuminata_pahang_v4.gff3
For metadata, same as above (with "MUSAC") - click "
Create dataset"
Note: you may also download files locally and either use the browser upload feature or upload them in the "volumes/data/upload" directory and use the uploaded file list.
So far, nothing special: just a dataset has been created and files should be in "volumes/data":
├── genoring │ ├── dts │ │ └── MUSAC │ │ └── pahang │ │ ├── .metadata │ │ │ ├── Musa_acuminata_pahang_v4.fasta.metadata │ │ │ └── Musa_acuminata_pahang_v4.gff3.metadata │ │ ├── Musa_acuminata_pahang_v4.fasta -> ../../../src/fasta/MUSAC/Musa_acuminata_pahang_v4.fasta │ │ ├── Musa_acuminata_pahang_v4.gff3 -> ../../../src/gff3/MUSAC/Musa_acuminata_pahang_v4.gff3 │ │ └── pahang_assembly.tsv │ └── src │ ├── fasta │ │ └── MUSAC │ │ ├── .metadata │ │ │ └── Musa_acuminata_pahang_v4.fasta.metadata │ │ └── Musa_acuminata_pahang_v4.fasta │ └── gff3 │ └── MUSAC │ ├── .metadata │ │ └── Musa_acuminata_pahang_v4.gff3.metadata │ └── Musa_acuminata_pahang_v4.gff3 ├── .htaccess └── upload
You can go back to the shell to enable more modules:
# ./genoring.pl enable genoringtools -no-backup- it will build GenoRing tools container and enable it.
# ./genoring.pl enable jbrowse -no-backup- it will build GenoRing JBrowse container and enable it.
Note: if you try to enable JBrowse first, it will complain GenoRing Tools module is not enabled.
Now go back on the website and edit the "Pahang" dataset: you should now have a "Data models > Genome Assembly > JBrowse" section.
If you did not restart GenoRing, you should see a button "Load assembly in JBrowse", otherwise stop GenoRing and restart it in "backend" mode (# ./genoring.pl stop && ./genoring.pl backend).
- click on the button "
Load assembly in JBrowse" - you should now have a top menu "
JBrowse pahang" leading to a JBrowse page
If you want to see Gigwa, you will have to enable Mongo module first:
# ./genoring.pl enable mongodb42 -no-backup- adjust environment and validate
# ./genoring.pl enable gigwa -no-backup- adjust environment and validate ("Direct access" avoids embedding Gigwa into the GenoRing site)
You should now have a top menu "Gigwa", but current integration does not allow to do anything at the moment.
Consider this release as a "proof of concept" which still requires a lot of work and polishing. GitHub issues will be update next week to reflect the work plan, and list missing features and known bugs.
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