It seems like modification of 'citation_url' in the universe_wsgi.ini config file has no effect in the UI (Help --> How to Cite Galaxy). Is it something hard-coded in the source?
we're hosting our own galaxy instance and the next step should bei the
integration of GeneTrack. (Not the tool, that is already included, but
the browser, which has to be set up on our own, as i could read on the
I've been reading all information on http://genetrack.bx.psu.edu and
http://atlas.bx.psu.edu/genetrack/docs/genetrack.html - but I do not
really get, which is the current, newest version? The only one to
download is available at googlecode (1.0.3) and - according to the
information on http://genetrack.bx.psu.edu - there is a newer one (2.0)
I tried to run the tests for 1.0.3 but some fail - the logs aren't quite
clear about the problem, even on Debug-mode.
Could you tell me what version to use and which instructions? Are there
limits or other dependencies according to the used python-packages?
Hoping for help & thanks in advance,
I'm getting exactly the same problem with any job running on a TORQUE/PBS
cluster. The jobs actually run fine as I can see the output and download
it, but it's marked as failed in the galaxy history, with the following
WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako)
cannot be fetched
The command `python -ES ./scripts/fetch_eggs.py` gives nothing as output.
If I run the same tools locally there is no problem.
> Message: 5
> Date: Thu, 27 Oct 2011 15:08:17 +1100
> From: Jerico Nico De Leon Revote <jerico.revote(a)monash.edu>
> To: galaxy-dev(a)lists.bx.psu.edu
> Subject: [galaxy-dev] Local Galaxy Instance MarkupSafe error
> Content-Type: text/plain; charset="iso-8859-1"
> I'm just doing a simple get->data from UCSC on our local Galaxy
> instance and got the following error:
> WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako)
> cannot be fetched
> The job box then is displayed as red on the history panel.
> The job runner states that the job finished normally on the cluster.
> Galaxy is checkout from galaxy-central (changeset: 6176:34fffbf01183).
I have been trying to figure out how to make the changes you suggested (i.e. write output files to the job_working_directory) and then move them over to files but I am having a difficult time navigating the code. If you could point me in the right direction, that would be helpful. I know the lib/galaxy/models/__init__.py initializes the output files but I don't think that is the right place to make the change. This change probably needs to be done in the Job_Wrapper but most of the code is very cryptic to me. Any guidance would be greatly appreciated. These changes should not take very long to implement once I get a handle on the code.
Ilya Chorny Ph.D.
Bioinformatics Scientist I
9885 Towne Centre Drive
San Diego, CA 92121
I am trying to get job's index in the history panel using SQL query (index number shown in the history when a job is submitted). I am unable to locate the necessary table-column for it. Any pointers in which table-column it is located will be really helpful.
Hello Galaxy Folks,
NCBI has received a few requests to provide a mechanism for people browsing the NCBI databases to download the data they have selected into Galaxy, so we are looking into it. I know some other sites have done this, it looks like through a URL based callback mechanism.
However, I know things can change over time, and I'd like to be sure that we are assessing an approach that reflects your current best thinking, whether it turns out to be something well established you are happy with, or if you might be considering moving toward something new, we'd like you to tell us what you think would work best for your users in your environment.
If you can just point me at a URL with the appropriate documentation, that's great. If you'd prefer to dialog a little, we're happy to talk. If there is a particular person we should be talking to, let me know.
Thanks for your help.
James M. Ostell, Ph.D.
Chief, Information Engineering Branch
National Center for Biotechnology Information, NLM, NIH
Bldg 45, Rm 5AN.44A
45 Center Drive
Bethesda, MD 20892-6510
I have an in-house Perl tool that generates a double digit number of
outputs that we'd like the user to have access to, but don't
necessarily need to be in the history. A complicating factor is that
the exact number is determined at run time as user input can add any
number of outputs that can't be determined in the scope of the tools'
Ideally, the end result would be that executing the tool would produce
a single output in the history with the other files either being
hidden or in the extra_files path. The visible file should be an HTML
file that can be used to describe and link to the other outputs as
well as providing the option to either unhide or add the hidden
outputs to the history for use in subsequent analysis.
I've looked at composite datatypes, but as far as I can tell the
documentation and examples don't cover how to produce a composite
datatype with a variable number of outputs. I briefly tried to use
the deprecated <code> tag to iterate over the results with the other
outputs added as hidden extra files to the index after execution, but
wasn't really excited about using a deprecated feature and couldn't
get it working quickly, regardless. Any other suggestions?
Masonic Cancer Center
University of Minnesota
I am very new to Galaxy and so far have only used the online interface.
However, I have an old Unix-running computer and I was hoping to run
Galaxy as a local instance. However, the computer has a very small hard
drive, that is already half full, so I was wondering if there is any way I
can run Galaxy by installing it on an external hard drive. I tried
already, and was able to install it properly and connect, but I get errors
when I try to upload data.
Any help would be greatly appreciated. I don't have a lot of experience
with Unix systems, so it might be something easy to solve or impossible to
do, I have no idea.