On Jan 12, 2012, at 11:41 PM, Ryan Golhar wrote:
Any ideas as to how to fix this? We are interested in using Galaxy to host
all our NGS data. If indexing on the head node is going to happen, then this
is going to be an extremely slow process.
Could you post the contents of
Hi Jeremy,
sorry for bother you again. I do some tests and the problem seems
not in the semi-colons (the cheetah manual is not very clear in
this sense, I put them but it did not solve the problem), but in the
display tag which is simply incorrect in that position, a call to
a python script is
I re-uploaded 3 BAM files using the Upload system filepaths
On Fri, Jan 13, 2012 at 10:53 AM, Nate Coraor n...@bx.psu.edu wrote:
On Jan 12, 2012, at 11:41 PM, Ryan Golhar wrote:
Any ideas as to how to fix this? We are interested in using Galaxy to
host all our NGS data. If indexing on the
I re-uploaded 3 BAM files using the Upload system file paths. runner0.log
shows:
galaxy.jobs DEBUG 2012-01-13 12:50:08,442 dispatching job 76 to pbs runner
galaxy.jobs INFO 2012-01-13 12:50:08,555 job 76 dispatched
galaxy.jobs.runners.pbs DEBUG 2012-01-13 12:50:08,697 (76) submitting file
May you suggest me how to sketch a simple python script that prints in the
central section of the galaxy
window a message like you are not authorized to execute this tool ?
This isn't possible right now, hence my reference to the open Bitbucket issue
regarding this limitation.
The best you
i had seen the job process die with this error:
if state != old_state:
UnboundLocalError: local variable 'state' referenced before assignment
since the DRM timeout is an intermittent error, i'm not absolutely positive
i have nailed it (a bit more time will tell -- i'm keeping an eye on it
correction: i didn't adequately test what happens if the user_proj_map_db
was not defined in the universe file; here's the changes:
157 # BEGIN ADD USER'S PROJ
158 try:
159 conn = sqlite3.connect(self.app.config.user_proj_map_db)
160 c = conn.cursor()
161
I've corrected this problem in change set 6510:3d9f0ce7bb61, which is running
on both the Galaxy main and test tool sheds. Thanks for reporting this issue.
Greg Von Kuster
On Jan 11, 2012, at 5:10 PM, Anthonius deBoer wrote:
Im trying to install a tool from the toolshed that showed me this
Hi,
I'm trying to use the update.py script and is not clear for me what to
use for 'url' in the usage line:
usage: create.py key url [key=value ...].
Which I'm guessing is just a carry over from create.py.
I tried passing the direct link to the dataset:
$ ./update.py my_key
