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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
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until the documentation is written.
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Set these options in galaxy.ini and start the server:
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admin_users = you@example.org
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library_import_dir = /path/to/some/directory
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In the directory you specified for 'library_import_dir', create some
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subdirectories, and put (or symlink) files to import into Galaxy into those
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subdirectories.
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In Galaxy, create an account that matches the address you put in 'admin_users',
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then browse to that user's preferences and generate a new API Key. Copy the
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key to your clipboard and then use these scripts:
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% ./display.py my_key http://localhost:4096/api/libraries
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Collection Members
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------------------
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0 elements in collection
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% ./library_create_library.py my_key http://localhost:4096/api/libraries api_test 'API Test Library'
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Response
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--------
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/api/libraries/f3f73e481f432006
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name: api_test
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id: f3f73e481f432006
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% ./display.py my_key http://localhost:4096/api/libraries
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Collection Members
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------------------
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/api/libraries/f3f73e481f432006
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name: api_test
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id: f3f73e481f432006
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% ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006
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Member Information
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------------------
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synopsis: None
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contents_url: /api/libraries/f3f73e481f432006/contents
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description: API Test Library
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name: api_test
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% ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents
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Collection Members
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------------------
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/api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
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name: /
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type: folder
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id: 28202595c0d2591f61ddda595d2c3670
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% ./library_create_folder.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1'
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Response
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--------
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/api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
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name: api_test_folder1
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id: 28202595c0d2591fa4f9089d2303fd89
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% ./library_upload_from_import_dir.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19
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Response
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--------
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/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
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name: 2.bed
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id: e9ef7fdb2db87d7b
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/api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
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name: 3.bed
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id: 3b7f6a31f80a5018
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% ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents
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Collection Members
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------------------
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/api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
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name: /
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type: folder
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id: 28202595c0d2591f61ddda595d2c3670
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/api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
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name: /api_test_folder1
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type: folder
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id: 28202595c0d2591fa4f9089d2303fd89
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/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
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name: /api_test_folder1/2.bed
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type: file
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id: e9ef7fdb2db87d7b
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/api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
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name: /api_test_folder1/3.bed
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type: file
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id: 3b7f6a31f80a5018
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% ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
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Member Information
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------------------
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misc_blurb: 68 regions
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metadata_endCol: 3
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data_type: bed
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metadata_columns: 6
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metadata_nameCol: 4
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uploaded_by: nate@...
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metadata_strandCol: 6
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name: 2.bed
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genome_build: hg19
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metadata_comment_lines: None
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metadata_startCol: 2
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metadata_chromCol: 1
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file_size: 4272
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metadata_data_lines: 68
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message:
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metadata_dbkey: hg19
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misc_info: uploaded bed file
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date_uploaded: 2010-06-22T17:01:51.266119
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metadata_column_types: str, int, int, str, int, str
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Other parameters are valid when uploading, they are the same parameters as are
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used in the web form, like 'link_data_only' and etc.
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The request and response format should be considered alpha and are subject to change.
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