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.
--nate
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