Question about compressed files
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
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:
-- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruening@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/
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.
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:
Thank you for explaining it further, Jeremy. We'll keep that in mind next time we use that method. Anyway, I'm sorry for this redundant post, but I'm getting an error every time I am uploading a file into a data library using my non-admin user account. Galaxy says that there is no valid file within the user directory. The file I am uploading is a .fq file. I've made the necessary changes in universe_wsgi.ini and gave the necessary permissions to my user account. What could be causing that error? Thanks again! CL
participants (3)
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Björn Grüning -
Ciara Ledero -
Jeremy Goecks