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
add_key command, and consists of tab-delimited
lines with three fields:
demo http://127.0.0.1:8080 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
By default the API keys are not shown by
--show-api-keys option to include them.
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
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
nebulizer remove_key ALIAS