Ryan Golhar wrote:
> Hi all - I'm uploading datasets into my local instance by importing
> from the filesystem w/o copying into Galaxy.
> Importing of uncompressed files works properly.  The files I'm
> importing are owned by user1 and a read-able by everyone, including
> the galaxy user.  The galaxy user does not have write permissions in
> the directory where the files are stored.
> I have fastq files that are compressed with gzip and owned by user1.
> I don't want Galaxy to uncompress them, but it appears it is trying
> to during import, and subsequently fails because of permissions.
> Is there a way I can force galaxy to import the compressed files w/o
> uncompressing them?  I think most of the mapping programs work on
> compressed fastq files so I'd rather not uncompressed them to save
> space.

Galaxy doesn't currently have a way to know whether a tool supports
compressed data or not - most do not, but as you mention, some do.
Because of this, all files are decompressed on upload.

To prevent this, you'd need to comment out the section of
tools/data_source/upload.py that does the decompression, which is the
code under:

    elif is_gzipped and is_valid:
        # We need to uncompress the temp_name file, but BAM files must remain 
compressed in the BGZF format

But this will cause problems with filetype autodetection and setting
metadata which may take a fair amount of time to work around.


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