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check your universe_wsgi.ini file:
# Allow users to remove their datasets from disk immediately (otherwise,
# datasets will be removed after a time period specified by an
administrator in
# the cleanup scripts run via cron)
Hi,
Maybe my message was not understandable enough. I really need your help, so
I'll try to be more concise :
How do I make a composite output from 2 datatypes that I have declared myself ?
I've followed the Composite Datatypes wiki but it seems that I've missed
something...
My composite
Hi all,
I am looking for instructions to migrate users, configuration and data
to other Galaxy machine. I have a production Galaxy, with users,
histories, pages, data libraries, configured tool panel, running on a
postgresdb. I want to move this information to a fresh Galaxy install
(same
Hi everyone
The Galaxy system as described in Belinda Giardine et al's 2005 Genome
Research paper (Galaxy: A platform for interactive large-scale genome
analysis) appears to be radically different from the current Galaxy, at
least in its technical specification. The paper mentions a C core spoken
Hi Joachim
This is roughly what we did ~15 months ago:
1. make a copy of the MySQL DB (postgresdb in your case)
2. copy the complete galaxy directory to the new server (make sure you
keep the path)
3. point the new galaxy server to the DB copy and start it (different
port number)
-
Hi Peter
Have a look at Anton's talk Introduction to Galaxy at last years GCC
meeting: http://wiki.g2.bx.psu.edu/Events/GCC2011
The first few slides are talking about the history of Galaxy, eg:
Galaxy as a single Perl script (!)
Regards, Hans
On 06/12/2012 01:28 PM, Peter van Heusden
And Galaxy had a predecessor called Gala, probably also implemented in perl.
Belinda may also have published a paper about Gala.
Bob H
On Jun 12, 2012, at 8:36 AM, Hans-Rudolf Hotz wrote:
Hi Peter
Have a look at Anton's talk Introduction to Galaxy at last years GCC
meeting:
Hi Hans-Rudolf,
Thank you for sharing your experience!
To summarize:
1. user information is stored in the database (histories, pages,
workflows). This info is linked to the datasets,
2. all datasets are in the '../database/files' (or the location
specified in universe_wsgi.ini) directory,
On 06/12/2012 04:04 PM, Joachim Jacob wrote:
Hi Hans-Rudolf,
Thank you for sharing your experience!
To summarize:
1. user information is stored in the database (histories, pages,
workflows). This info is linked to the datasets,
2. all datasets are in the '../database/files' (or the location
We are going in circles here :)
Me:
my hope is for a way of programmatically importing and updating new tools
You:
This is currently possible (and very simple to do) using the Galaxy Admin UI
I would call using the Admin UI not doing some programmatically.
You have done a brilliant job making
Hi
I'm developing tools that use an entry in the tool_data_table_config.xml file.
For upload into a repository I created a tool_data_table_config.xml.sample file
with the corresponding table entry. The structure for the file I copied from
the tool_data_table_config.xml. in the galaxy
Hi Birgit,
I don't see any problem with your xml definition below. Are you sure the
problem is not with another file in the tarball? If you can send me the
tarball, I'll take a look.
Greg Von Kuster
On Jun 12, 2012, at 4:09 PM, Birgit Crain wrote:
Hi
I'm developing tools that use an
Thanks, Greg
I tried uploading the same tar ball without the
tool_data_table_config.xml.sample file and the tools load fine (to troubleshoot
I added only tools that actually do not depend on the file). As soon as I add
the .sample file to the tar ball I get the error message.
Thanks, Birgit
Thank you, Greg. I'll see it right away.
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Another question, Nate. After running Galaxy, I had problems with accessing
the data in the created upload folder. Is there anything else that I need
to do?
Thank you so much for all the help.
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Dear John
This sounds interesting, however, I've been struggling for quite a sometimes on
limiting the number of options a user could see when it loads the tool wrapper.
I have a separate database that records the results obtained from the execution
of my developed tool along with the
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