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/> > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
