Quickstart¶

Log in as your user, navigate to the API Keys page in the User menu, and generate a new API key. Make a note of the API key, and then pull up a terminal. Now we’ll use the display.py script in your galaxy/scripts/api directory for a short example, which assumes your local galaxy server is running on the default port 8080:

% ./display.py my_key http://localhost:8080/api/histories
Collection Members
------------------
#1: /api/histories/8c49be448cfe29bc
  name: Unnamed history
  id: 8c49be448cfe29bc
#2: /api/histories/33b43b4e7093c91f
  name: output test
  id: 33b43b4e7093c91f

The result is a Collection of the histories of the user specified by the API key (you). To look at the details of a particular history, say #1 above, do the following:

% ./display.py my_key http://localhost:8080/api/histories/8c49be448cfe29bc
Member Information
------------------
state_details: {'ok': 1, 'failed_metadata': 0, 'upload': 0, 'discarded': 0, 'running': 0, 'setting_metadata': 0, 'error': 0, 'new': 0, 'queued': 0, 'empty': 0}
state: ok
contents_url: /api/histories/8c49be448cfe29bc/contents
id: 8c49be448cfe29bc
name: Unnamed history

This gives detailed information about the specific member in question, in this case the History. To view history contents, do the following:

% ./display.py my_key http://localhost:8080/api/histories/8c49be448cfe29bc/contents
Collection Members
------------------
#1: /api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a
  name: Pasted Entry
  type: file
  id: 6f91353f3eb0fa4a

What we have here is another Collection of items containing all of the datasets in this particular history. Finally, to view details of a particular dataset in this collection, execute the following:

% ./display.py my_key http://localhost:8080/api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a
Member Information
------------------
misc_blurb: 1 line
name: Pasted Entry
data_type: txt
deleted: False
file_name: /Users/yoplait/work/galaxy-stock/database/files/000/dataset_82.dat
state: ok
download_url: /datasets/6f91353f3eb0fa4a/display?to_ext=txt
visible: True
genome_build: ?
model_class: HistoryDatasetAssociation
file_size: 17
metadata_data_lines: 1
id: 6f91353f3eb0fa4a
misc_info: uploaded txt file
metadata_dbkey: ?

And now you’ve successfully used the API to request and select a history, browse the contents of that history, and then look at detailed information about a particular dataset.

For a more comprehensive Data Library example, set the following options in your galaxy.yml as well, and restart galaxy again:

admin_users: you@example.org
library_import_dir: /path/to/some/directory

In the directory you specified for ‘library_import_dir’, create some subdirectories, and put (or symlink) files to import into Galaxy into those subdirectories.

In Galaxy, create an account that matches the address you put in ‘admin_users’, then browse to that user’s preferences and generate a new API Key. Copy the key to your clipboard and then use these scripts:

% ./display.py my_key http://localhost:8080/api/libraries
Collection Members
------------------

0 elements in collection

% ./library_create_library.py my_key http://localhost:8080/api/libraries api_test 'API Test Library'
Response
--------
/api/libraries/f3f73e481f432006
  name: api_test
  id: f3f73e481f432006

% ./display.py my_key http://localhost:8080/api/libraries
Collection Members
------------------
/api/libraries/f3f73e481f432006
  name: api_test
  id: f3f73e481f432006

% ./display.py my_key http://localhost:8080/api/libraries/f3f73e481f432006
Member Information
------------------
synopsis: None
contents_url: /api/libraries/f3f73e481f432006/contents
description: API Test Library
name: api_test

% ./display.py my_key http://localhost:8080/api/libraries/f3f73e481f432006/contents
Collection Members
------------------
/api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
  name: /
  type: folder
  id: 28202595c0d2591f61ddda595d2c3670

% ./library_create_folder.py my_key http://localhost:8080/api/libraries/f3f73e481f432006/contents 28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1'
Response
--------
/api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
  name: api_test_folder1
  id: 28202595c0d2591fa4f9089d2303fd89

% ./library_upload_from_import_dir.py my_key http://localhost:8080/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19
Response
--------
/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
  name: 2.bed
  id: e9ef7fdb2db87d7b
/api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
  name: 3.bed
  id: 3b7f6a31f80a5018

% ./display.py my_key http://localhost:8080/api/libraries/f3f73e481f432006/contents
Collection Members
------------------
/api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
  name: /
  type: folder
  id: 28202595c0d2591f61ddda595d2c3670
/api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
  name: /api_test_folder1
  type: folder
  id: 28202595c0d2591fa4f9089d2303fd89
/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
  name: /api_test_folder1/2.bed
  type: file
  id: e9ef7fdb2db87d7b
/api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
  name: /api_test_folder1/3.bed
  type: file
  id: 3b7f6a31f80a5018

% ./display.py my_key http://localhost:8080/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
Member Information
------------------
misc_blurb: 68 regions
metadata_endCol: 3
data_type: bed
metadata_columns: 6
metadata_nameCol: 4
uploaded_by: nate@...
metadata_strandCol: 6
name: 2.bed
genome_build: hg19
metadata_comment_lines: None
metadata_startCol: 2
metadata_chromCol: 1
file_size: 4272
metadata_data_lines: 68
message:
metadata_dbkey: hg19
misc_info: uploaded bed file
date_uploaded: 2010-06-22T17:01:51.266119
metadata_column_types: str, int, int, str, int, str

Other parameters are valid when uploading, they are the same parameters as are used in the web form, like ‘link_data_only’ and etc.

The request and response format should be considered alpha and are subject to change.