Thanks for the screenshot.
That page will often and regrettably report errors when there are
none. I think the advice I have been given by people who know the tool
shed better is to click install and then leave that page and go to the
list of installed repositories to track progress.
Did that
Hi Team,
I have installed GATK2 into a galaxy cloud instance to use the Unified
Genotyper for our sequencing course. However, when I run the tool I get the
following error message:
Dataset 41: Unified Genotyper on data 8 and data 13 (VCF)
Tool execution generated the following error message:
Hi Marcus,
There was some discussion of proxies a while ago - and it looks like
people were able to get it to work, does this advice help any?
http://dev.list.galaxyproject.org/How-to-install-tool-shed-behind-proxy-with-authentication-td4663218.html
As for the install and test framework - I am
Hi,
Do we have a way (or plans) for sharing tool parameter settings in Galaxy?
I know the following workarounds :
* Share a history with all users: so users can import your step and do
rerun to run on their own file with your settings
* Wrap the step in a workflow with all
Hi Robert,
Can you check on CloudMan's Admin page if the following is shown (towards
the bottom of the page): Switch master to not run jobs
If it says, Switch master to run jobs, just click on the text and the
master will become an execution host on the cluster, which should then give
Galaxy some
Hi Enis,
I have indeed set the master node to not run jobs. Does there has to be at
least one execution host (either master or always on worker) auto scaling to
work?
Thanks for the help,
Robert
From: Enis Afgan [afg...@gmail.com]
Sent: Thursday, October 09,
There needs to be at least one exec host for jobs to actually run,
irrespective of whether auto-scaling is on or off.
In an attempt to offload work from the master instance when there are
workers, CloudMan will automatically toggle the master as an exec host a
the first worker is added or the
I am trying to resolve an issue with snpEff 3.4 running on a cloudman instance
of galaxy. The instance is invoking the following command and failing:
java -Xmx6G -jar $SNPEFF_JAR_PATH/snpEff.jar eff -c
$SNPEFF_JAR_PATH/snpEff.config -i vcf -o vcf -upDownStreamLen 5000
-spliceSiteSize 1 -stats
Hey there
Using the new upload tool my data uploads but never appears in the
history. All I can see in paster.log when I do an upload is:
10.8.0.2 - - [09/Oct/2014:20:43:58 +0200] POST /tool_runner/index
HTTP/1.0 200 - https://phillipl.sanbi.ac.za/root; Mozilla/5.0 (X11;
Ubuntu; Linux x86_64;
Ulf,
Thanks for all the information, hopefully it helps me replicate this issue
so I can figure out a better fix.
I can work on some better documentation for this, but there aren't any
Galaxy-specific instructions that I know of. Using the basic configuration
for setting up the rabbitmq server
Hi Folks,
I suspect I know the answer to this question already, but I have to ask
just for the sake of completeness...
I'm working on a tool for which I'd like to query an external server for
the set of expected inputs, and then make that set available as input
options. The tool in question
This was asked a few years ago but no takers: Galaxy Tool Development:
(http://dev.list.galaxyproject.org/Reading-user-id-before-the-execution-of-the-tool-td4490324.html)
Seems like this isn't possible, unless there's a way to plant user's name in a
text field on the tool's form, so that a
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