On Mon, Jan 12, 2015 at 10:24 PM, Peter Cock <> wrote:
Hi Ryan,

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 <> 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 <>
> 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?
>> Peter
>> On Mon, Jan 12, 2015 at 4:52 PM, Ryan G <>
>> wrote:
>> > Galaxy is not decompressing the file.  The file is linked to on the
>> > filesystem.
>> >