mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Greg Von Kuster
cf96dccddb
This feature is now available for any installable revision of a repository using the new "Export this revision" option in the Repository actions menu in the browser. It is also available via the Tool Shed API using a command like the following: export.py --url http://testtoolshed.g2.bx.psu.edu --name chemicaltoolbox --owner bgruening --revision 4133dbf7ff4d --export_repository_dependencies True --download_dir /tmp
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.