Storing and managing Galaxy API keys

The majority of Nebulizer’s commands require valid credentials in order to interact with a Galaxy instance. These can be supplied explicitly on the command line each time:

nebulizer -u USER@DOMAIN [ -P PASSWORD ] ...command...
nebulizer -k API_KEY ...command...

Alternatively it is possible to store Galaxy URL-API key pairs in a file called .nebulizer located in the user’s home directory, with each pair being associated with an alias.

The file is created automatically the first time an alias is created using add_key command, and consists of tab-delimited lines with three fields:


for example:

demo   4551fbf7cd8b1bc59db....

This file can be manually edited using a text editor such as vi; however Nebulizer also provides a set of commands for querying and modifying the file contents.

list_keys shows the aliases with their associated Galaxy URLs:

nebulizer list_keys


By default the API keys are not shown by list_keys; use the --show-api-keys option to include them.


Use the whomai command to find out which user is associated with an alias:

nebulizer whoami ALIAS

add_key will store a Galaxy-API key combination under a new alias. If the API key is known then the general form of the command is:

nebulizer add_key ALIAS GALAXY_URL API_KEY

However it is usually easier to get Nebulizer to fetch the key automatically, by supplying a Galaxy username (email):

nebulizer -u USER@DOMAIN add_key ALIAS GALAXY_URL

Multiple Galaxy URL-key pairs can be stored; only the associated aliases need to be unique.

update_key will update the details stored for an existing alias:

nebulizer update_key ALIAS --new-url GALAXY_URL
nebulizer update_key ALIAS --new-api-key API_KEY
nebulizer -u USER@DOMAIN update_key ALIAS --fetch-api-key

remove_key deletes an existing ALIAS and associated credentials:

nebulizer remove_key ALIAS