Welcome to the Pop Up Browser

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Scope of Purpose

- visualize personal data
- get started on collaboration quickly
- start on hosted site

Notes on the size of the Jetstream VM

- small is best for hosting (slow use of SUs)
- medium is required for loading large genome references
The solution here one of two options:
- you can start as medium image, set up the browser, image the VM (through JS interphase), and then relaunch as a small VM
- you can have two VMs, one large and one medium. Use the medium VM to set up the browser, test, etc as needed, and shut it down when you aren't using it. You can then use the small VM to run constantly, which will reduce the consumption of your allocation. Moving files from dev (M) to production (S) is pretty easy with Globus. Contact help@ncgas.org or see ncgas.org tutorials for more information on this.

Features

PopUp JBrowse
BLAST w JBrowse links
Tripal Job Daemon
Links that persist despite dynamic IP allocation
GUI creation and linking of BLAST databases with JBrowse instances

Set Up and Use

JBrowse:
- see Help for PopUp JB
- once you have built it, add link to GENOME BROWSERS tab (edit the page, fill in the URL and title for the button to work!)

BLAST:
- make a blast reference using the tool under Genome Browsers
- you can pre-upload the reference file (fa) to /var/www/html/sites/default/files (via globus or jetstream shell/web gui)
- add reference (add content -> Blast Database)
You can also upload a pre-made blast database if you'd like, but it will not automatically link to jbrowse.

If you are going public:
- change your password! Use a terminal shell (through JS or putty or terminal) to do the following:
cd /var/www/html/
sudo drush upwd --password="MyNewPassword" admin