That is the workaround I am using, which means keeping an uncompressed copy of the FASTQ file on our main storage from where Galaxy can see it (for people to use within their histories).
From a long term storage perspective this is not
ideal - so I am keen for better handling of gzipped files within Galaxy (particularly within libraries which we use for raw data).
On Mon, Jan 12, 2015 at 5:20 PM, Ryan G firstname.lastname@example.org wrote:
Yes, I'm doing a link to file on file system when doing a library import. Does this mean I should link to the the uncompressed file?
On Mon, Jan 12, 2015 at 12:14 PM, Peter Cock email@example.com wrote:
Ah. Then this is more subtle... are you using the library import option where Galaxy just symlinks to existing files? I thought that was not possible with gzipped files (for the reasons given below). Perhaps this is not being blocked, leading to the confused state you're seeing?
On Mon, Jan 12, 2015 at 4:52 PM, Ryan G firstname.lastname@example.org wrote:
Galaxy is not decompressing the file. The file is linked to on the filesystem.