Hi list,
Is there a currently a known problem with the "export to file" function? I'm trying to migrate some data from the public galaxy to a private one; the export function worked well with a small (~100mb) dataset, but it has not been working with larger datasets (>2GB) and I get the error: Server Error. An error occurred. See the error logs for more information. (Turn debug on to display exception reports here). Is there a limit on the file size of the export? If so, what is it?
Thanks in advance, Dave
Hi Dave,
To export larger files, you can use a different method. Open up a terminal window on your computer and type in at the prompt ($):
$ curl -0 '<file_link>' > name_the_output
Where <file_link> can be obtained by right-clicking on the disc icon for the dataset and selecting "Copy link location".
If you are going to import into a local Galaxy, exporting entire histories, or a history comprised of datasets that you have copied/grouped together, may be a quick alternative. From the history panel, use "Options (gear icon) -> Export to File" to generate a link, then use curl again to perform the download. The "Import from File" function (in the same menu) can be used in your local Galaxy to incorporate the history and the datasets it contains.
Hopefully this helps, but please let us know if you have more questions,
Jen Galaxy team
On 10/17/12 2:37 PM, Dave Corney wrote:
Hi list,
Is there a currently a known problem with the "export to file" function? I'm trying to migrate some data from the public galaxy to a private one; the export function worked well with a small (~100mb) dataset, but it has not been working with larger datasets (>2GB) and I get the error: Server Error. An error occurred. See the error logs for more information. (Turn debug on to display exception reports here). Is there a limit on the file size of the export? If so, what is it?
Thanks in advance, Dave
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Hi I have a local install of Galaxy on my desktop. I performed the following steps:
Created a new Library Selected "Upload directory of files" Chose the "server Directory" Selected "Copy files into Galaxy"
However, when I execute I get the following error. Any ideas?
Error Traceback: View as: Interactive | Text | XML (full) ⇝ AttributeError: 'Bunch' object has no attribute 'multifiles' URL: http://140.253.78.44/galaxy/library_common/upload_library_dataset Module weberror.evalexception.middleware:364 in respond view
app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__ view
environ, self.app)
Module paste.wsgilib:539 in intercept_output view
app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__ view
return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__ view
return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__ view
body = method( trans, **kwargs )
Module galaxy.web.controllers.library_common:855 in upload_library_dataset view
**kwd )
Module galaxy.web.controllers.library_common:1055 in upload_dataset view
json_file_path = upload_common.create_paramfile( trans, uploaded_datasets )
Module galaxy.tools.actions.upload_common:342 in create_paramfile view
multifiles = uploaded_dataset.multifiles,
AttributeError: 'Bunch' object has no attribute 'multifiles'
Do I need to set something else?
Thanks Neil
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