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:
alias|Galaxy_URL|API_key
for example:
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
URLs:
nebulizer list_keys
Note
By default the API keys are not shown by list_keys
;
use the --show-api-keys
option to include them.
Note
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