Galaxy assumes that tools that write to stderr indicate failure. There's
apparently some way
to set up regexps to get around that, but I don't know where to do that
(or if indeed that would work).
Command-line debugging works some, except when the web server's
environment (path, etc.)
differs
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
know
where to look. And my code needs to be able to, at the very least,
print debug messages. How do people generally do that in Galaxy?
Thanks
--Mark Johnson
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what tool_runner
is trying to do.
In short, how do you debug tools?
Thanks
--Mark Johnson
NCBI
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and othe
m using appears below. Instead of a download, I simply
get the Galaxy home page content (welcome.html) in the center
iframe, and no download.
Is it clear from the XML what I'm missing?
Thanks
--Mark Johnson
Staff Scientist
NCBI
On 3/19/12 5:19 PM, Peter Cock wrote:
Why do you need to do anything special at all for Galaxy here? I'd
just write it as a single command line call which blocks. As far as
Galaxy will know it is just a slow tool.
I suppose the tool could just poll the server, and only produce results
when t
, but most of what's in the
scripts in the tool files isn't documented.
Thanks
Mark Johnson
Staff Scientist, NCBI
mjohn...@ncbi.nlm.nih.gov
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