Hi,
I'm a Galaxy and Python newbie and I'm working on project that desires to upload files from a directory to the Galaxy server. We'd like to physically copy the files rather than maintain references to them.
I'm starting by following the examples in scripts/api/README. All the display and library_create_library examples work. However, the library_upload_from_import_dir fails. In my universe...ini, library_import_dir is defined to be /home/dgeorge/galaxy/import and there is a bed directory under that with a short file, bed1.bed in the correct format. I'm not sure what to provide for the last parameter, the dbkey - maybe that's my problem?
I ran:
./library_upload_from_import_dir.py 59d2fd4e020e178f8c48e61150e513c2 http://localhost:8080/api/libraries/f597429621d6eb2b/contents c6ca0ddb55be603a10e891fff2e902c3 bed bed hg19
And I get the error:
Exception happened during processing of request from ('127.0.0.1', 38857)
Traceback (most recent call last):
File "/home/dgeorge/galaxy/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/http server.py", line 1053, in process_request_in_thread
self.finish_request(request, client_address)
File "/usr/lib/python2.6/SocketServer.py", line 322, in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.6/SocketServer.py", line 618, in __init__
self.finish()
File "/usr/lib/python2.6/SocketServer.py", line 661, in finish
self.wfile.flush()
File "/usr/lib/python2.6/socket.py", line 297, in flush
self._sock.sendall(buffer(data, write_offset, buffer_size))
error: [Errno 32] Broken pipe
Any ideas or suggestions?
Thanks!
David George
Staff Software Engineer
Illumina, Inc.
25861 Industrial Blvd.
Hayward, CA 94545
Tel: 510-670-9326
Fax: 510-670-9302
Email: dgeorge@illumina.com mailto:dgeorge@illumina.com