JJ,
Arg this is a mess. I am very sorry about this - I still don't
understand extra_files_path versus files_path myself. There are open
questions on Peter's blast repo and no one ever followed up on my
object store questions about this with Bjoern's issues a couple
release cycles ago. We need to
Okay - so this is what broke things:
https://bitbucket.org/galaxy/galaxy-central/commits/d781366bc120787e201b73a4dd99b56282169d86
My feeling with the commit was that wrappers and tools should never be
explicitly accessing paths explicitly through input.dataset.*. I think
this would circumvent
I agree with you about the inadvisable use of: input.dataset.*.
I'm looking at:
lib/galaxy/model/__init__.py
class Dataset( object ):
...
def __init__( self, id=None, state=None, external_filename=None,
extra_files_path=None, file_size=None, purgable=True, uuid=None ):
...
Hey JJ,
Opened a pull request to stable with my best guess at the right to
proceed and hopefully a best practice recommendation we can all get
behind. Do you want to try it out and let me know if it fixes snpeff?
(It does fix the velvet datatypes you contributed to Galaxy.)
Hi John,
glad to see this gets some attention!
Am 15.10.2014 um 19:05 schrieb John Chilton:
Hey JJ,
Opened a pull request to stable with my best guess at the right to
proceed and hopefully a best practice recommendation we can all get
behind. Do you want to try it out and let me know if it
On Wed, Oct 15, 2014 at 1:47 PM, Björn Grüning
bjoern.gruen...@gmail.com wrote:
Hi John,
glad to see this gets some attention!
Am 15.10.2014 um 19:05 schrieb John Chilton:
Hey JJ,
Opened a pull request to stable with my best guess at the right to
proceed and hopefully a best practice
Looks good, John.
I tested with:
https://testtoolshed.g2.bx.psu.edu/view/jjohnson/snpsift_dbnsfp_datatypes
lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
reverting from hack:
command interpreter=pythontabular_to_dbnsfp.py $input
