Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

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:

% ./display.py my_key http://localhost:4096/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:4096/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:4096/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:4096/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 option in your galaxy.ini 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:4096/api/libraries
Collection Members
------------------

0 elements in collection

% ./library_create_library.py my_key http://localhost:4096/api/libraries api_test 'API Test Library'
Response
--------
/api/libraries/f3f73e481f432006
  name: api_test
  id: f3f73e481f432006

% ./display.py my_key http://localhost:4096/api/libraries
Collection Members
------------------
/api/libraries/f3f73e481f432006
  name: api_test
  id: f3f73e481f432006

% ./display.py my_key http://localhost:4096/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:4096/api/libraries/f3f73e481f432006/contents
Collection Members
------------------
/api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
  name: /
  type: folder
  id: 28202595c0d2591f61ddda595d2c3670

% ./library_create_folder.py my_key http://localhost:4096/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:4096/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:4096/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:4096/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.