Peter has already voted and if I recall correctly Ryan cannot access Trello - so this might be a waste to bring up - but here is a Trello card for voting on this issue and tracking progress https://trello.com/c/3RkTDnIn.
To summarize previous discussion - this would be fantastic to have and Galaxy needs this - but we solve this on usegalaxy.org by using a compressed file system - a more elegant solution when it is a possibility - so it has never been a tier one priority for the devteam. The only update on this is that I don't think we are using a compressed file system anymore so this might become and issue again someday soon.
This would be non-trivial to implement - but I have always felt this would be a fairly fun project to work on if anyone really tight on space locally wants to try to tackle it :).
-John
On Tue, Jan 13, 2015 at 9:54 AM, Ryan G ngsbioinformatics@gmail.com wrote:
Agreed.
On Mon, Jan 12, 2015 at 10:24 PM, Peter Cock p.j.a.cock@googlemail.com 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).
Peter
On Mon, Jan 12, 2015 at 5:20 PM, Ryan G ngsbioinformatics@gmail.com 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 p.j.a.cock@googlemail.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?
Peter
On Mon, Jan 12, 2015 at 4:52 PM, Ryan G ngsbioinformatics@gmail.com wrote:
Galaxy is not decompressing the file. The file is linked to on the filesystem.
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