Ryan Golhar wrote:
Hi all - I'm uploading datasets into my local instance by
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
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
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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fn:Ryan Golhar, Ph.D.
org:The Cancer Institute of NJ;Cancer Informatics Core/Bioinformatics
adr:5th floor;;120 Albany St;New Brunswick;NJ;08901;USA
title:NGS Bioinformatics Specialist
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