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. _______________________________________________ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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