[2] | 1 | This is not documentation. These are hints and examples to get you started |
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| 2 | until the documentation is written. |
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| 3 | |
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| 4 | Set these options in universe_wsgi.ini and start the server: |
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| 5 | |
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| 6 | enable_api = True |
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| 7 | admin_users = you@example.org |
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| 8 | library_import_dir = /path/to/some/directory |
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| 9 | |
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| 10 | In the directory you specified for 'library_import_dir', create some |
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| 11 | subdirectories, and put (or symlink) files to import into Galaxy into those |
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| 12 | subdirectories. |
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| 13 | |
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| 14 | In Galaxy, create an account that matches the address you put in 'admin_users', |
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| 15 | then browse to that user's preferences and generate a new API Key. Copy the |
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| 16 | key to your clipboard and then use these scripts: |
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| 17 | |
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| 18 | % ./display.py my_key http://localhost:4096/api/libraries |
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| 19 | Collection Members |
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| 20 | ------------------ |
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| 21 | |
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| 22 | 0 elements in collection |
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| 23 | |
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| 24 | % ./library_create_library.py my_key http://localhost:4096/api/libraries api_test 'API Test Library' |
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| 25 | Response |
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| 26 | -------- |
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| 27 | /api/libraries/f3f73e481f432006 |
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| 28 | name: api_test |
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| 29 | id: f3f73e481f432006 |
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| 30 | |
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| 31 | % ./display.py my_key http://localhost:4096/api/libraries |
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| 32 | Collection Members |
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| 33 | ------------------ |
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| 34 | /api/libraries/f3f73e481f432006 |
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| 35 | name: api_test |
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| 36 | id: f3f73e481f432006 |
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| 37 | |
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| 38 | % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006 |
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| 39 | Member Information |
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| 40 | ------------------ |
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| 41 | synopsis: None |
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| 42 | contents_url: /api/libraries/f3f73e481f432006/contents |
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| 43 | description: API Test Library |
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| 44 | name: api_test |
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| 45 | |
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| 46 | % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents |
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| 47 | Collection Members |
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| 48 | ------------------ |
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| 49 | /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 |
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| 50 | name: / |
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| 51 | type: folder |
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| 52 | id: 28202595c0d2591f61ddda595d2c3670 |
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| 53 | |
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| 54 | % ./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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| 55 | Response |
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| 56 | -------- |
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| 57 | /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 |
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| 58 | name: api_test_folder1 |
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| 59 | id: 28202595c0d2591fa4f9089d2303fd89 |
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| 60 | |
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| 61 | % ./library_upload_from_import_dir.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19 |
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| 62 | Response |
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| 63 | -------- |
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| 64 | /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b |
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| 65 | name: 2.bed |
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| 66 | id: e9ef7fdb2db87d7b |
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| 67 | /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 |
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| 68 | name: 3.bed |
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| 69 | id: 3b7f6a31f80a5018 |
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| 70 | |
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| 71 | % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents |
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| 72 | Collection Members |
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| 73 | ------------------ |
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| 74 | /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 |
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| 75 | name: / |
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| 76 | type: folder |
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| 77 | id: 28202595c0d2591f61ddda595d2c3670 |
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| 78 | /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 |
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| 79 | name: /api_test_folder1 |
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| 80 | type: folder |
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| 81 | id: 28202595c0d2591fa4f9089d2303fd89 |
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| 82 | /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b |
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| 83 | name: /api_test_folder1/2.bed |
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| 84 | type: file |
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| 85 | id: e9ef7fdb2db87d7b |
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| 86 | /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 |
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| 87 | name: /api_test_folder1/3.bed |
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| 88 | type: file |
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| 89 | id: 3b7f6a31f80a5018 |
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| 90 | |
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| 91 | % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b |
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| 92 | Member Information |
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| 93 | ------------------ |
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| 94 | misc_blurb: 68 regions |
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| 95 | metadata_endCol: 3 |
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| 96 | data_type: bed |
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| 97 | metadata_columns: 6 |
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| 98 | metadata_nameCol: 4 |
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| 99 | uploaded_by: nate@... |
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| 100 | metadata_strandCol: 6 |
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| 101 | name: 2.bed |
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| 102 | genome_build: hg19 |
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| 103 | metadata_comment_lines: None |
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| 104 | metadata_startCol: 2 |
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| 105 | metadata_chromCol: 1 |
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| 106 | file_size: 4272 |
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| 107 | metadata_data_lines: 68 |
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| 108 | message: |
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| 109 | metadata_dbkey: hg19 |
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| 110 | misc_info: uploaded bed file |
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| 111 | date_uploaded: 2010-06-22T17:01:51.266119 |
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| 112 | metadata_column_types: str, int, int, str, int, str |
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| 113 | |
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| 114 | Other parameters are valid when uploading, they are the same parameters as are |
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| 115 | used in the web form, like 'link_data_only' and etc. |
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| 116 | |
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| 117 | The request and response format should be considered alpha and are subject to change. |
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