Hi Galaxy,
I'm trying to put one of my java tool in galaxy.
I've copied the required files in my tool directory under /tools/jvarkit
(I can see it galaxy)
$ ls
commons-jexl-2.1.1.jar
commons-logging-1.1.1.jar
htsjdk-1.129.jar
snappy-java-1.0.3-rc3.jar
vcffilterjs.jar
that why I
asked about the error log)
Thank you for your help
PS: By the way, my argument was -e 'variant!=null;' , why do I see '-e
'variant!=nullX' in the log ?
Pierre
On Thu, Feb 26, 2015 at 10:59 AM, Pierre Lindenbaum
wrote:
Hi Galaxy,
I'm trying to
> You'll need to white list the semi-colon which Galaxy has replaced as
a security precaution (user free text can be exploited). See
here: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Peter
Thanks: adding :
On 02/26/2015 02:51 PM, John Chilton wrote:
Just to make sure - since it hasn't been explicitly stated - is this
tool being installed from the tool shed? The environment variable
setup in tool_dependencies.xml will only be available for tool shed
installs.
no, my future plan is to put it in the
On 02/26/2015 03:43 PM, John Chilton wrote:
Sorry I wasn't clear about that - it hasn't reached galaxy-dist yet -
you can download the latest snapshot of 15.03 release (I believe it is
running on usegalaxy.org as of yesterday) via this link instead
https://bitbucket.org/galaxy/galaxy-central/get/
On 02/26/2015 04:20 PM, John Chilton wrote:
Well - this version does feature Sam's complete rewrite of the front
end for tools - so things will be pretty different.
Oddly though your tool loaded for me - can you open up your JavaScript
console and let me know if there are any errors?
my bad, e
Hi all, I got a "Internal Server Error" ==> "KeyError:
'tool_panel_section' " when I'm trying to install a new tool from our
toolshed (see stacktrace below).
My galaxy instance was cloned from
commit 217854827ac7dfc88c5388cd2ecb24fffd86c060
Merge: 056a7e0 ad0d0bc
Author:
Soranzo
Date: Wed Nov 18 10:06:53 2015 +
I was able to install my tool from this toolshed a few minutes ago.
The second attempt failed.
Thanks for the helps,
Pierre
thanks
M.
On Wed, Oct 19, 2016 at 9:20 AM Pierre Lindenbaum
<mailto:pierre.lindenb...@univ-nantes.fr>> wrote:
On 10/19/2016 03:36 PM, Martin Čech wrote:
Hi Pierre,
It seems that instead of uninstalling you de-activated the repository.
I would uninstall the repository again.
admin > manage installed tools > there is no tool installed.
Search toolshed > select > >> preview and install > "Install
That worked !
Many thanks !
At the top of the 'manage installed tools' page there is a filter that
hides uninstalled and deactivated tools. Click 'advanced search' and
then 'Deactivated or uninstalled'. Do you see your tool deactivated there?
M.
On Wed,
(cross-posted at https://biostar.usegalaxy.org/p/20220/ )
I'm trying to create some `tools.xml` that use java.
Those tools need to download some library (*.jar) files from
http://central.maven.org/ and I want to create a variable
$MYTOOLCLASSPATH containing the jars. I've tried the following
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 would
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 ag
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