Question: Shared Data Library Access Problem
gravatar for danielfortin86
2.8 years ago by
United States
danielfortin86110 wrote:


On our local instance of Galaxy we've installed several data Libraries that are symlinked. For some reason now, we cannot access them when clicking on the links (from Shared Data ->Data Libraries or "Admin->Data Libraries"). Possibly relevant information: the webserver is running Apache. From the paster.log file, I get the following:

Traceback (most recent call last):

File "/opt/galaxy/eggs/Paste-", line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File "/usr/lib64/python2.6/", line 332, in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib64/python2.6/", line 628, in __init__
File "/usr/lib64/python2.6/", line 671, in finish
File "/usr/lib64/python2.6/", line 303, in flush
self._sock.sendall(buffer(data, write_offset, buffer_size))
error: [Errno 32] Broken pipe

Does anyone have any ideas as to what;s wrong here?



data library • 774 views
ADD COMMENTlink written 2.8 years ago by danielfortin86110

That seems like a generic connecting error that might be caused by the original file path being inaccessible now. Can you check whether the target files are in the place?

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Martin Čech ♦♦ 4.9k

Yes, the files are still there and can be reached by using the account that runs galaxy. The files are symlinked though, could that have something to do with it?

ADD REPLYlink written 2.8 years ago by danielfortin86110

So the target files are themselves symlinks? Your setup is still unclear to me. Please explain.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Martin Čech ♦♦ 4.9k

Sorry for the confusion, when I add a directory to a Shared Library, galaxy looks in directories related to the email address of the user (e.g. /remote/users/galaxy/upload/ for specific sub-directories. For that reason, if I wish to allow the user to add files in a directory to his shared library, I create a symlink in the location /remote/users/galaxy/upload/ which points to somewhere else on the file system. Then when the user clicks on "Shared Data" he can add files from this link. This has been working fine until recently. Please let me know if further explanation is required.

ADD REPLYlink written 2.8 years ago by danielfortin86110
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