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.c...@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 <ngsbioinformat...@gmail.com> > wrote: > > Galaxy is not decompressing the file. The file is linked to on the > > filesystem. > > > > On Mon, Jan 12, 2015 at 10:28 AM, Peter Cock <p.j.a.c...@googlemail.com> > > wrote: > >> > >> Hi Ryan, > >> > >> The problem isn't Galaxy stripping the extension, rather > >> Galaxy is actually decompressing the file as part of the > >> upload process. > >> > >> Unfortunately (and there is an open Trello enhancement > >> request on this), Galaxy does not support sorting any of > >> the defined datatypes in compressed form UNLESS they > >> are defined that way (like BAM files). > >> > >> This has lead some Galaxy Admins to define a new datatype > >> lgzippedfastq (or similar - I'd have to check my old emails > >> for the exact name used as a gripped alternative to the > >> Galaxy sangerfastq datatype) and then modified many/all > >> their tools to handle this. That is a lot of work, but does > >> offer big disk savings for this key datatype. > >> > >> The Galaxy team instead use a compressed file system, > >> so for usegalaxy.org ALL their data files are compressed > >> but Galaxy can ignore this complexity. > >> > >> Peter > >> > >> On Mon, Jan 12, 2015 at 3:15 PM, Ryan G <ngsbioinformat...@gmail.com> > >> wrote: > >> > Hi all - I've got a bunch of fatsq files uploaded into a data library > in > >> > Galaxy. The underlying files is gzipped however Galaxy strips the .gz > >> > from > >> > the filename and displays it as .fastq. When the python wrapper > >> > rgFastQC.py > >> > gets called, it correctly sees the fastq.gz file. The wrapper > creates a > >> > symbolic link to the .gz file in a tmp directory. The link is .fastq. > >> > When > >> > FastQC tries to read this file, it fails because its compressed. So > one > >> > of > >> > two things is going wrong here: > >> > > >> > 1) It looks like the wrapper is incorrectly renaming the file, but > its > >> > using the name given to it in Galaxy. > >> > > >> > 2) When the file is uploaded into the data library, Galaxy is > stripping > >> > off > >> > the .gz extension. > >> > > >> > I think #2 is the more correct problem. How can I keep Galaxy from > >> > stripping the .gz extension? > >> > > >> > ___________________________________________________________ > >> > 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: > >> > https://lists.galaxyproject.org/ > >> > > >> > To search Galaxy mailing lists use the unified search at: > >> > http://galaxyproject.org/search/mailinglists/ > > > > >
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