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 <ngsbioinformatics@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?
>

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