mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
117 lines
3.7 KiB
Plaintext
117 lines
3.7 KiB
Plaintext
This is not documentation. These are hints and examples to get you started
|
|
until the documentation is written.
|
|
|
|
Set these options in universe_wsgi.ini and start the server:
|
|
|
|
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.
|