Problem to link bam files when uploading through system paths
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/>
Zhibin Lu wrote:
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,
Hi Zhibin, Thanks for catching this! It has been fixed in changeset 5947:4b3fefa396cf --nate
--
*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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participants (2)
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Nate Coraor -
Zhibin Lu