Thank you Paul and Nate. We will try the options you suggested.
One thing we found to work much faster (less than 5 minutes for most files) is to upload zipped data. Galaxy could upload and unzip the files without any problem. It doesn't seem any sequence data is lost. Has anyone tried this before?
Thanks.
Tilahun ---------------
Nate Coraor wrote:
Paul-Michael Agapow wrote:
From: Tilahun AbebeTilahun.Abebe@uni.edu
We are trying to load Illumina data to our local Galaxy instance. The files are between 700 MB and 2.2 GB. Files below 2 GB load in less
than
5 minutes. Files larger than 2 GB don't upload at all. We installed Galaxy locally because we thought loading files will be faster than
the
server version. Any suggestions to solve this problem is highly
appreciated.
While (from others experience) Galaxy _should_ be able to upload files that large, we've had some problems with our local installation too. Investigation didn't reveal any cause, so we put it down to the quality of our network. You might what to look at the webserver or proxy that you have in front of Galaxy - from memory, both Apache and nginx can be configured to impose file size limits, so that _may_ be the problem. In any event, you might want to configure your server to handle uploads and downloads directly as per https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServe r. Finally you can pass an url to the upload dialog to get Galaxy to pull the file from an ftp server - for example - and that may prove more robust.
Hi Paul,
These failures may be due to the fact that many browsers will simply fail to upload files> 2GB (although I know there are people out there have successfully done it).
Tilahun, I'll echo Paul's suggestion to use the Production setup. There are also alternative options for getting data into Galaxy. For users, you can have an FTP server (or just a local directory on the server where they can place files for upload):
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/UploadViaFTP
Or you can use data libraries and load directly off filesystems accessible to the server:
https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFile...
--nate
Paul Agapow (paul-michael.agapow@hpa.org.uk) Bioinformatics, Centre for Infections, Health Protection Agency
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