Hi,
We are doing a puppet configuration for our Galaxy service and this includes
installing tools with the "install_tool_shed_repositories.py" script. It seems
that when we specify a revision for a tool which is not the latest we get an
error
e.g.
/usr/bin/python
/OSM/galaxy/tools/galaxy-de
See: https://trello.com/c/YBK8ZPFb/
Hopefully one of the Galaxy team can take a look.
Peter
On Wed, Oct 21, 2015 at 3:48 PM, Marco Ocana wrote:
> Thanks for you help Peter.
> I have reported the problem using the built in Galaxy reporting tool from
> one of my failed jobs.
> I also created a Tr
Thanks for you help Peter.
I have reported the problem using the built in Galaxy reporting tool from
one of my failed jobs.
I also created a Trello bug submission.
Regards,
Marco
On Wed, Oct 21, 2015 at 10:15 AM, Peter Cock
wrote:
> Thanks Marco,
>
> OK, that seems to still be part of the Gala
Thanks Marco,
OK, that seems to still be part of the Galaxy core:
https://github.com/galaxyproject/galaxy/blob/dev/tools/genomespace/genomespace_importer.xml
I think you need to file a bug with the main GitHub repository (or Trello).
Looking at genomespace_importer.xml I don't see how the hidde
Hi Peter,
I am getting the metadata for the tool from:
https://usegalaxy.org/api/tools/genomespace_importer
Thanks
Marco
On Wed, Oct 21, 2015 at 8:01 AM, Peter Cock
wrote:
> Hi Marco,
>
> I'd lay money on the the tool parameter sanitization done in Cheetah
> intended to avoid any command ins
Here is the pull request: https://github.com/galaxyproject/galaxy/pull/823
You can see what file was edited
On Wed, Oct 21, 2015 at 8:40 AM, Floreline TOUCHARD <
floreline.touch...@gmail.com> wrote:
> Thank you ! Can you tell me which files are to update or download ?
> I installed my applicati
Hi Floreline,
The files from Ryan's pull request are visible here:
https://github.com/galaxyproject/galaxy/pull/823/files
It's a pretty simple change to enable some extra debugging information that
might help you discover the cause of your issue.
On 10/21/2015 07:40 AM, Floreline TOUCHARD wrot
Thank you ! Can you tell me which files are to update or download ?
I installed my application on a server that was not open to the outside.
Currently I do not support different versions or updates of my application
with git.
I can download the files to edit and transfer them to the server but not
Hi Marco,
I'd lay money on the the tool parameter sanitization done in Cheetah
intended to avoid any command insertion into the shell command.
This can be configured within the tool definition using the
tag set:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E_tag_set
A brief writeup of my experiences:
http://web.science.mq.edu.au/~cassidy/wordpress/2015/10/21/galaxy-tool-generating-datasets/
Steve
On 21 October 2015 at 18:27, Peter van Heusden wrote:
> These names have meaning in CollectedDatasetMatch:
>
> designation means designation if that exists else
I just recently submitted a patch that will display all the environment
variables being passed to Galaxy in pastor.log. That should help you determine
if the variables are set and to what.
Please excuse any typos -- Sent from my iPhone
> On Oct 21, 2015, at 6:11 AM, Floreline TOUCHARD
> wr
Hi,
I've got an issue with my external authentication configuration. I use
Apache and the mod_perl
modules (AuthenNIS + AuthzNIS + Net-NIS) to authenticate to galaxy with NIS
accounts.
I have the authentication form when I try to access galaxy web page.
But after a successful authentication it
These names have meaning in CollectedDatasetMatch:
designation means designation if that exists else name
name means name
dbkey means dbkey
ext means ext
visible means visible
On 21 October 2015 at 08:44, Steve Cassidy wrote:
> Thanks, yes that works, though I'm not really sure what the differ
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