failure in name resolution'}
Cheers,
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
e...@msi.umn.edu
boll0...@umn.edu
___
Please keep all
for a production environment?
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
e...@msi.umn.edu
boll0...@umn.edu
___
Please keep all replies on the list
Thanks Dave,
Everything is back to normal again.
Cheers,
-E
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
e...@msi.umn.edu
boll0...@umn.edu
On Tue, Nov 11, 2014 at 2:20 PM, Dave Bouvier d
Is there an API endpoint for sending the error report for a failed
step in a history? I would like to run a workflow via API and email
the first error that occurs.
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter
to be in brackets (e.g.,
[10.32.16.121]). Is there an option to configure the from address
format, or override the address?
If there are no configuration options, what files would I need to
modify to add brackets? The domain name is not an option.
Cheers,
-Evan Bollig
Research Associate | Application
When I run a workflow and multiple steps fail, does Galaxy have the
option to send a digest of all problems, or does each failed step
result in another email? Or maybe only the first failed task results
in an email alert?
I'm trying not to get spammed when a workflow fails.
Cheers,
-Evan Bollig
I'm using bioblend to launch a workflow, but i find that the
gi.workflows.run_workflow() command does not provide an option for
no_wait.
Can anyone provide justification for why this needs to be synchronous?
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Jobs executed in the workflow appear to have a creation time, but no
execution start and end time listed. How does one determine when
something executed? I'd like to know exactly where the time is spent
computing...
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Thanks Dannon. I'll add it to the todo list. Do the metric include
time and memory info for the entire history/workflow, or does it only
report for individual tools? Max consumed storage during a workflow
execution is another data point I'd like to monitor.
-E
-Evan Bollig
Research Associate
if the package_gatk_1_4 could also
install those R libraries itself.
Cheers,
-E
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
e...@msi.umn.edu
boll0...@umn.edu
On Tue, Jul 29, 2014 at 4:22 PM, Björn Grüning
Btw, I forgot: plyr_1.7.1 is also required for package_gatk_1_4. Hence
the install_url call for it below.
-E
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
e...@msi.umn.edu
boll0...@umn.edu
I want to install ggplot2 into package_r. The library ggplot2 is no
longer available from the CRAN mirror for R v2.11.0. How do you guys
handle this situation?
Can I install another package_r and have packages that depend on
package_r_2_11_0 use the newer version?
-Evan Bollig
Research Associate
much on your package. Is it not
possible to use a newer R version? In either case you should save all
tarballs somehow to archive them!
Cheers,
Bjoern
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
I don't know all the subtleties of the galaxy workflow syntax. My goal
is to specify the default input file names for a number of tools in a
workflow. Is this possible, or am I limited to only providing the file
type or extension?
If possible, can you provide an example?
Thanks,
-Evan Bollig
dozens of files that are txt for
example. I want to know all possible tool_state annotations for Input
Dataset (tool_id: null). Where would I find this?
Cheers,
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612
itself.
Cheers,
-E
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
e...@msi.umn.edu
boll0...@umn.edu
On Thu, Jun 12, 2014 at 7:36 AM, Shrum, Donald C dcsh...@admin.fsu.edu wrote:
I've setup
job_conf.xml is outside of my knowledge. Better wait to see what the
others can tell us.
-E
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
e...@msi.umn.edu
boll0...@umn.edu
On Thu, Jun 12, 2014
/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
e...@msi.umn.edu
boll0...@umn.edu
). If the
parameter new_tool_panel_section_label specifies the section_name,
what option exists to specify the label? Or perhaps was the *_label
option intended to provide the subheading and another option (e.g.,
new_tool_panel_section_name supposed to exist)?
Cheers,
-Evan Bollig
Research
I notice that the galaxy web api for installing tools from the
toolshed does not include any entrypoint for uninstalling tools. This
must be intentional, but what was the motivation to leave this out?
Cheers,
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Hey Greg,
I see that option in the galaxy web UI, but I am working from the
command line and scripting against your toolshed web api. Its the api
that is missing the uninstall option for repositories/tools.
https://wiki.galaxyproject.org/ToolShedApi
Cheers,
-E
-Evan Bollig
Research Associate
just merge the old code back in and submit a pull request, or
I also see that a few scripted calls to
scripts/api/install_tool_shed_repositories.py should also take care of
it.
Cheers,
-E
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing
I am working in the galaxy-dist stable branch. I select a workflow and
select Delete. An alert pops up asking if I'm sure I want to do
that. I press Cancel and the alert disappears, along with the
workflow. This shouldn't happen.
Cheers,
-Evan Bollig
Research Associate | Application Developer
clean --all to make sure I was
working with a fresh install.
Cheers,
-E
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
e...@msi.umn.edu
boll0...@umn.edu
On Fri, May 16, 2014 at 2:39 PM, Dannon
upgrade step be included
automatically when the initial DB build fails?
This is the first time a DB is being built, so it should be dead simple
Cheers,
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624
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