> Is there an easy way to add meta data to a dataset without having to resort
> to coding it into the dataset definition?
> I am looking for things beyond tags and just a simple key value pair
> association would be enough...
Tags support key-value pairs using this syntax:
--
key:value
OR
key
Hi Jim,
This is nice and is a path forward for the immediate future.
That said, a couple extensions to Galaxy to better support composite datatypes
would enable cummerbund without the additional tools:
(i) extending the composite datatype to include definition of individual
outputs in the coll
Hi all:
After updating our local galaxy installation to the latest build last week,
I found that when tophat finished its execution, all its output files showed
empty in the history.
However, I could execute the exact same command via shell and got correct
tophat output files.
It seeme
How should I configure my local galaxy to allow access to sub-files in
/datasets/[hashcode]/display/? FastQC is still broken on the latest build.
This issue was reported by others as well.
David Hoover
Helix Systems Staff, CIT/NIH
Begin forwarded message:
> From: David Hoover
> Date: Septem
When running CCAT I get:
Error running CCAT.
Traceback (most recent call last):
File "/opt/Galaxy/tools/peak_calling/ccat_wrapper.py", line 44, in
if __name__ == "__main__": main()
File "/opt/Galaxy/tools/peak_calling/ccat_wrapper.py", line 41, in main
return stop_err( tmp_dir, e )
Hi,Is there an easy way to add meta data to a dataset without having to resort to coding it into the dataset definition?I am looking for things beyond tags and just a simple key value pair association would be enough...I cannot see anything that is obvious, but I feel something must be there...Than
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
On Thu, Oct 11, 2012 at 6:14 PM, Jim Johnson wrote:
> Checking to see if there is any interest in including a parameter option to
> select outputs for cuffdiff,
> potentially including a composite output and a cummeRbund sqlite database.
>
Hi JJ,
I'm highly interested in something like this, I e
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
Some additional info;
Actually the errors already started at migrate version 93->94.
I just restored the version to prior upgrade to check any other errors. There
were some create errors. I am not sure if these come from the \n\t statements
in the sysntax or whether that is just an error log outp
Checking to see if there is any interest in including a parameter option to
select outputs for cuffdiff,
potentially including a composite output and a cummeRbund sqlite database.
Issues:
cuffdiff produces 21 output files, which is a little unwieldy in a galaxy
history.
cummeRbund generates
Hi all!
The "accordion" style would be very nice for me and my user base.
Cheers,
Sascha
Original Message
processed by CONSOLIDATE
Subject:
Re: [galaxy-dev] Tool Menu Behavior
Sent:
Donnerstag, 11. Oktober 2012 23:44
From:
Jeremy Goecks (jeremy.goe...@emory.edu)
Carrie,
Currently,
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