You can get to the captured stdout/stderr in the UI by clicking the
info (i) button for the dataset. The way I would normally debug
outside of the Galaxy UI is to take the command line generated by
Galaxy (which should be logged) and run it outside Galaxy.
-- jt
On Fri, Oct 12, 2012 at 9:35 AM,
Galaxy does indeed print a lot of log data to stdout (when not in
daemon mode). But when something fails, it's just an exception;
sometimes it's clear what it means, sometimes not. My problem is I
can't get print debugging to work. Galaxy captures both stdout and
std
Mark, how are you running your Galaxy instance, and have you changed
the value of log_level in your universe_wsgi.ini? By default Galaxy
should be provide quite verbose logging on stdout.
-- jt
On Wed, Oct 10, 2012 at 2:21 PM, Mark Johnson wrote:
> I'm trying to add CSRA (NCBI Compressed Sequen
My comments inline...
On Oct 10, 2012, at 4:39 PM, John Chilton wrote:
> Comments inline.
>
> On Wed, Oct 10, 2012 at 2:35 PM, Mark Johnson
> wrote:
>>
>> Thanks for the quick turnaround. On the contrary, your examples are very
>> helpful. I'll try your approach. I haven't upgraded Galaxy in
Comments inline.
On Wed, Oct 10, 2012 at 2:35 PM, Mark Johnson wrote:
>
> Thanks for the quick turnaround. On the contrary, your examples are very
> helpful. I'll try your approach. I haven't upgraded Galaxy in about 6
> months, but was hoping that change had already been made. (I haven't worked
Hey Mark,
A few things, instead of printing stuff out you could use the global
variable log in the binary.py file. Maybe something like
log.warn("SNIFFING csra"). I think your logging statements will be
more likely to show up then.
I don't know why what you are doing won't work (it looks like it
I'm trying to add CSRA (NCBI Compressed
Sequence Read Archive) as a new datatype for Galaxy.
I've followed the instructions on the wiki, and the module seems
to load OK. csra shows up as a datatype in the upload view.
But the upload fails, and the up
