That makes sense as BAM files are compressed. My files though are fastq. I don't think (or know) that BAM files can be used as input to mapping programs.

On 2/28/11 4:01 AM, Christian Hundsrucker wrote:
Hi Ryan,

thnx for the response. I figured out that this is/sould be solved for
.bam files
I just don't understand how...

Best,
Christian

see .../lib/galaxy/datatypes/binary.py

[...]
     def sniff( self, filename ):
         # BAM is compressed in the BGZF format, and must not be
uncompressed in Galaxy.
         # The first 4 bytes of any bam file is 'BAM\1', and the file is
binary.
         try:
             header = gzip.open( filename ).read(4)
             if binascii.b2a_hex( header ) == binascii.hexlify( 'BAM\1' ):
                 return True
             return False
         except:
             return False
[...]

Ryan Golhar wrote:
No, I never got a response to this...post it to the list and see what
comes out of it...

On 2/25/11 3:59 AM, Christian Hundsrucker wrote:
Hi Ryan,

did you get an answer to your questions which didn't appear in the
mailing-list?
I have a similar Problem:
want to load a R-workspace within a galaxy module (.rdat-file,
R-Project) and therefore built the galaxy-.rdat datatype (binary).
.rdat-files are gzipped and are only recognized within R if they are
still zipped...

Would be happy for any aswer!
If the answer is "no" I'll add this problem to the mailing list.

Thnx,
Christian

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.


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