Name: vagrant-galaxy
Owner: Biological Informatics CoE @ Agriculture and Agri-Food Canada
Owner: Biological Informatics CoE @ Agriculture and Agri-Food Canada
Description: Vagrant provisioning a Galaxy development environment in an Ubuntu VM
Created: 2014-07-26 17:25:58.0
Updated: 2016-04-29 16:33:20.0
Pushed: 2016-11-07 18:39:29.0
Size: 60
Language: Shell
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Vagrant launcher for Galaxy (http://galaxyproject.org/)
Note - the easiest way to install Fabric is through pip (or easy_install):
install fabric fabtools
clone https://github.com/AAFC-MBB/vagrant-galaxy.git
vagrant-galaxy
rant up
Point your browser at http://localhost:8080/ after starting up the galaxy server. You can do this via fabric (see below), for convenience, or you can do it manually like so:
rant ssh
/galaxy
un.sh --daemon
To start the galaxy server, the included fabric file provides some convenience functions.
vagrant galaxy:start
Likewise, there are options for stopping, restarting, and checking the status of the galaxy server.
vagrant galaxy:stop
vagrant galaxy:restart
vagrant galaxy:status
You can find a full list of available fabric functions by typing the following:
list
Running a toolshed server inside the local VM is a convenient way to run deployment tests for your custom galaxy tools. You can develop your tool (including wrappers, tests, datatypes, dependencies, etc) on the galaxy instance, then upload the package to the toolshed and test installing it back on the galaxy instance.
The syntax is identical to starting the galaxy server:
vagrant toolshed:start
vagrant toolshed:stop
vagrant toolshed:restart
vagrant toolshed:status
Simply create a new user in each webapp with that e-mail address to access the admin menus (or add your own admin user to the config files).
This feature is still in development, but the basic usage is as follows:
vagrant config:OPTION,VALUE
See the config/config.yml [VM] section for supported VM configuration options. See the config/config.yml [Galaxy] section galaxy options that get set on provisioning. Hence, modifying the galaxy section after the VM is provisioned will not alter Galaxy's configuration.
Vagrant launcher for Galaxy (http://galaxyproject.org/)
Note - the easiest way to install Fabric is through pip (or easy_install):
install fabric fabtools
clone https://github.com/AAFC-MBB/vagrant-galaxy.git
vagrant-galaxy
rant up
Point your browser at http://localhost:8080/ after starting up the galaxy server. You can do this via fabric (see below), for convenience, or you can do it manually like so:
rant ssh
/galaxy
un.sh --daemon
To start the galaxy server, the included fabric file provides some convenience functions.
vagrant galaxy:start
Likewise, there are options for stopping, restarting, and checking the status of the galaxy server.
vagrant galaxy:stop
vagrant galaxy:restart
vagrant galaxy:status
You can find a full list of available fabric functions by typing the following:
list
Running a toolshed server inside the local VM is a convenient way to run deployment tests for your custom galaxy tools. You can develop your tool (including wrappers, tests, datatypes, dependencies, etc) on the galaxy instance, then upload the package to the toolshed and test installing it back on the galaxy instance.
The syntax is identical to starting the galaxy server:
vagrant toolshed:start
vagrant toolshed:stop
vagrant toolshed:restart
vagrant toolshed:status
Simply create a new user in each webapp with that e-mail address to access the admin menus (or add your own admin user to the config files).
This feature is still in development, but the basic usage is as follows:
vagrant config:OPTION,VALUE
See the config/config.yml [VM] section for supported VM configuration options. See the config/config.yml [Galaxy] section galaxy options that get set on provisioning. Hence, modifying the galaxy section after the VM is provisioned will not alter Galaxy's configuration.