Hello,
When i try to upload bam files into galaxy data library though system
paths with "link to files without copying into galaxy" option, galaxy
always complains that
"The uploaded files need grooming, so change your*Copy data into
Galaxy?*selection to be*Copy files into Galaxy*instead of*Link to files
without copying into Galaxy*so grooming can be performed."
no matter if the bam files are sorted or not.
in galaxy-dist/tools/data_source/upload.py:
285: if dataset.type in ( 'server_dir', 'path_paste' ) and
link_data_only == 'link_to_files':
286: # Never alter a file that will not be copied to Galaxy's
local file store.
287: if datatype.dataset_content_needs_grooming( output_path ):
288: err_msg = 'The uploaded files need grooming, so change
your <b>Copy data into Galaxy?</b> selection to be ' + \
289: '<b>Copy files into Galaxy</b> instead of <b>Link
to files without copying into Galaxy</b> so grooming can be performed.'
The 'output_path' is alwasy *None* when using *'link_to_files'*, so the
grooming check always returns False.
I think we need to check the original bam file instead at line 287 like:
*287: if datatype.dataset_content_needs_grooming( databset.path ):*
And the following code also needs to change:
314: if datatype.dataset_content_needs_grooming( output_path ):
315: # Groom the dataset content if necessary
316: datatype.groom_dataset_content( output_path )
A quick dirty fix would be:
*314: if not (dataset.type in ( 'server_dir', 'path_paste' ) and
link_data_only == 'link_to_files') and
datatype.dataset_content_needs_grooming( output_path ):
*
Please advise,
--
*Zhibin Lu*
Bioinformatics Support
*Ontario Institute for Cancer Research*
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3
Tel: 647-260-7944
Toll-free: 1-866-678-6427
www.oicr.on.ca <http://www.oicr.on.ca/>
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