Hello,
What worked for us was this action sequence :
- stop Galaxy
- update config/tool_sheds_file.xml (change the URL from the old one to
the new one)
- “sed” shed_tool_conf.xml to change the “guid", the tool_shed and the
“file” to replace the old prefix
Does anybody have any idea about this? To summarize, if a user imports data
from a shared data library and clicks on the pop-up to start analyzing
their data they are redirected to the login page even though they are
already logged in. Is there a setting to change this?
Thanks
On Sun, Oct 16,
I am currently working to create a wrapper for the MISO tools and wanted
to see if anyone has previously developed a functional or
semi-functional wrapper for it.
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Hi Mohamed,
“$__user_email__” is filled in by galaxy when generating the command line,
so you can directly refer to this in your command line.
See
https://github.com/galaxyproject/tools-iuc/blob/master/tools/tool_factory_2/rgToolFactory2.xml#L12
Dear all,
I would like to send as a parameter the name of the user (either user email
or username).
I tried in my xml file the option
But I have in results
X__user_email__
Any clue ?
Thanks in advance,
Mohamed
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Please
Thanks Peter,
it works, now
I've moved my xml to the way you've suggested **and** I had to change
the name of my environment_variable. I don't know why but I suspect
there is a 'ghost/persistent' (?) version of my variable that still
exists(!?) somewhere from a previous attempt.
Thank you
On 10/20/2016 11:06 AM, Peter Cock wrote:
Hi Pierre,
The first example looks OK, very similar to this one of mine for example,
so I am not sure what is breaking:
https://github.com/peterjc/pico_galaxy/blob/133aea82c02adf5509134c415565ada99c519312/tools/effectiveT3/tool_dependencies.xml
I
This wouldn’t be a transfer, you would uninstall the tools coming from the
old toolshed and re-install them form the new toolshed.
This is only possible if these tools are available from the second toolshed.
To illustrate the procedure, this is what you would do if you would take
all tools from
Hello Marius,
Thank you for your answer.
Are you sure that ephemeris can transfer tool from toolshed1 to
toolshed2 ? We read that it was only implemented to install tools from a
toolshed on a Galaxy.
We will try the second solution and as we already tried to manipulate
the database, we
Hi Youssef,
the tool shed url is also stored in the database, that's why just changing
the shed_tool_conf.xml is not working. I think you have a bunch of options
here:
1: You can make a list of tools from that toolshed and re-install them from
the new toolshed.
Hi there
I'm trying to add a wrapper for the vcftools vcf-consensus tool. There is
an existing tool collection for vcftools in tools-devteam, so I'm add it
there. Wrapper is at:
https://github.com/pvanheus/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus
I tested this
Hi Galaxy users,
As somebody try to run dynamic runner with the option
embed_metadata_in_job set to False ?
I notice that it works with drmaa runner but not with dynamic.
Here is my job_conf.xmf :
python
my_conf
False
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