Hi Ciara,

Galaxy supports compressed files like gz [1] by default. Keep in mind that large files like yours are not guaranteed to upload properly, please use other techniques to get your data in galaxy.

For example with FTP: http://wiki.g2.bx.psu.edu/FTPUpload

Hope that helps, Bjoern

[1] .gz/.gzip, .bz/.bzip, .bz2/.bzip2, zip

Hi all,

My colleague tried to upload via filesystem path a file with an approximate size of 2GB. It was a compressed file (filename.fq.gz). No error was reported, so I thought everything went fine, but when he tried running a tool, the uploaded file did not show in the input dropdown. But when he tried again, this time using an uncompressed file, every thing worked well. Now to my question: by default, can Galaxy accept and use compressed files? Or do I have to change something in its configuration just to do so?

Thanks for the help!

CL ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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When using the 'upload via filesystem path' option for data libraries, Galaxy will use the file "as is" without decompressing it. In practice, this means that you'll need to decompress it before uploading it to a library because Galaxy tools expect the dataset to be uncompressed.

This is, of course, different behavior than seen when uploading a compressed dataset. In that case, Galaxy will decompress the dataset as needed.

Best, J.

On Jul 4, 2012, at 5:10 AM, Ciara Ledero wrote:

Thanks for the quick reply.

I've already checked how to configure our Galaxy instance for FTP upload, but due to security reasons, I cannot use that option. I read the wiki for Data Libraries and found that uploading via filesystem path can be used for putting files with size greater than 2GB in Galaxy. Since the data is stored in the same place where our Galaxy is installed, choosing the link option in Upload via Filesystem path seemed good enough. Anyway, at least now I'm sure that Galaxy indeed accepts compressed files.

Again, thanks. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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