1) One more question,
My colleague likes the idea, but his composite data set dataset_id.dat file
contains only a plain list of uploaded files, not HTML like yours.
I was wondering if it is possible to pass somehow a parameter to
CompositeMultifile.regenerate_primary_file(dataset) to switch
On Mon, Oct 22, 2012 at 8:52 AM, David van Enckevort
david.van.enckev...@nbic.nl wrote:
Hi,
On the main galaxy page there is a link 'Report Issue' to the bitbucket
issue tracker, however since a few weeks it is not possible to view or
report issues anymore since it requires membership of the
Hello,
I have recently had the opportunity to look at the deployment of Galaxy
together with Apache, and I saw that the recommendation is to run the
Galaxy Web server behind Apache with the latter acting as a proxy:
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
Other than
Hey Greg Galaxy Team,
Galaxy doesn't load tool sections from multiple files in a consistent
manner. This is a minimal example that demonstrates the problem:
https://bitbucket.org/jmchilton/galaxy-central-tool-load-example
https://bitbucket.org/jmchilton/galaxy-central-tool-load-example/compare
On Mon, Oct 22, 2012 at 4:23 PM, David Hoover hoove...@helix.nih.gov wrote:
How does Galaxy determine that a job has failed?
It now depends on the individual tool's XML file.
Does it simply see if the STDERR is empty?
Why default, yes. The tool's XML can specify particular regexs
to look for,
On Oct 22, 2012, at 3:52 AM, David van Enckevort david.van.enckev...@nbic.nl
wrote:
On the main galaxy page there is a link 'Report Issue' to the bitbucket issue
tracker, however since a few weeks it is not possible to view or report
issues anymore since it requires membership of the
On Fri, Oct 19, 2012 at 8:57 PM, Scott McManus scottmcma...@gatech.edu wrote:
Ok -it's in. Thanks again! I will add a to-do item to put output-merge
messages
into stdout so that they're more visible.
-Scott
Great, thanks.
I see Edward Kirton had already reported the underlying problem
Hello,
I am a JBrowse Dev hoping to add the ability to export data directly from
JBrowse (JavaScript) to Galaxy (without exporting from JBrowse, saving
locally, opening Galaxy, loading file from drive). I have looked through the
wiki page on Data
By default Galaxy checks stderr, if it's not empty - returns an error. So if
your tool doesn't fail (returns 0) but you print something to stderr , your
tool will still fail in Galaxy. There's stderr_wrapper.py workaround for
that.
On the other hand, if you tool returns non zero but
The API allows you to do some of that...
If you pass it the ID of the object (input.id) you can do all kinds of requests
with the API.
Look in the scripts/api folder of your local Galaxy instance...
NOTE: The API seems to be a bit of a stepchild, since there is no good
documentation and it
Hi,
I am trying to automatically move certain outputs from my workflow into a
particular folder of a particular library THROUGH THE API.
I can find how to do the reverse, but can't find an example of how to do this...
Is there an equivalent of passing the history ID, like you can pass the
API seems a bit of overkill, as I understand, it's useful for 'external' access
via http. My tools run inside Galaxy and I should be able to use Python code
directly.
From: Anthonius deBoer [mailto:thondeb...@me.com]
Sent: Tuesday, 23 October 2012 12:16 PM
To: Khassapov, Alex (CSIRO IMT,
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