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/httpserver.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