Bjoern,
The following patch should put out the fire...
https://bitbucket.org/galaxy/galaxy-central/commits/d781366bc120787e201b73a4dd99b56282169d86
TL;DR - After this patch $output.extra_files_path is the same thing as
$output.files_path - which is to say not broken in a bunch of corner
cases an
Nate, John,
that bug bites me with so many tools. Next one is MACS2
Traceback (most recent call last):
File
"/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
line 153, in prepare_job
job_wrapper.prepare()
File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.
I can confirm this is error. Switching the tool to use
$outfile.files_path instead of $outfile.extra_files_path improves the
situation in my testing.
I thought for sure .extra_files_path had been deprecated in terms of
files_path - but the only Trello card I could find indicates the
opposite may b
Hi Nate,
we encountered an addition bug related to the object-store:
Traceback (most recent call last):
File "/usr/local/galaxy/galaxy-
dist/lib/galaxy/jobs/runners/__init__.py", line 153, in prepare_job
job_wrapper.prepare()
File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py
Hi Nate,
yes that is fixing it for me!
Thanks!
Bjoern
Am 12.06.2014 16:26, schrieb Nate Coraor:
writeable (e.g. what you have new_files_path set to), that'd confirm it.
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Hi Björn,
I believe the problem is most likely this bug:
https://trello.com/c/OHlQoCrx
If you symlink /usr/local/galaxy/galaxy-dist/database/tmp to somewhere
writeable (e.g. what you have new_files_path set to), that'd confirm it.
I'm going to take a look at fixing this today.
--nate
On
Hi,
I have configured to use the hierarchical object store but as soon as I try
to reset the filetpye of a dataset Galaxy is crashing with:
galaxy.objectstore DEBUG 2014-06-12 14:39:21,180 Using preferred backend
'files3' for creation of MetadataFile 5963
132.230.153.57 - - [12/Jun/2014:14:39:20
