Hi all,
While trying to install tools from the toolshed via the browser interface, an
error keeps appearing and nothing is abled to be installed. Currently using the
latest version of Galaxy and having tried to install several different tools,
the following error keeps appearing in the log file
I think you may have hit the same bug I found recently:
https://github.com/galaxyproject/galaxy/issues/3084
What is line 44 of your integrated_tool_panel.xml file?
Peter
On Thu, Nov 3, 2016 at 2:16 PM, Yip, Miu ki wrote:
> Hi all,
>
> While trying to install tools from the toolshed via the bro
Hello Miuki,
this looks like your integrated_tool_panel.xml file has some problems.
Can you try to move this file to a different location and try the
installation again?
It should be located in your galaxy directory.
Best,
Marius
On 11/03/2016 03:16 PM, Yip, Miu ki wrote:
Hi all,
While try
Hi Marius,
Thanks for the reply!
I have tried moving the file and just deleting the file all together. I am
still running into this error.
Thanks,
Miuki
> On Nov 3, 2016, at 10:29 AM, Marius van den Beek
> wrote:
>
> Hello Miuki,
>
> this looks like your integrated_tool_panel.xml file has
Dear Galaxy Developers,
Because of specific use case, our transfer tool need to keep the datasets
in a different location instead of the default location, so we'd like to
purge datasets according to its "external_filename" (we found this column
in the dataset table in the database). Is there a way
Good news - this is the bug I though it was, the ampersand
should be escaped as & in the XML file:
https://github.com/galaxyproject/galaxy/issues/3084
More good news: This will likely be fixed in the next release
of Galaxy:
https://github.com/galaxyproject/galaxy/pull/3122
Right now I suggest y
Awesome! After changing “&” to “and”, it worked!
Thank you!
> On Nov 3, 2016, at 12:59 PM, Peter Cock wrote:
>
> Good news - this is the bug I though it was, the ampersand
> should be escaped as & in the XML file:
>
> https://github.com/galaxyproject/galaxy/issues/3084
>
> More good news: Thi
Hey everyone,
I haven’t got a feedback from you.
If you have any suggestions, I’m a little bit confused with this problem.
Thank you very much!
Edgar Fernandez
System Administrator (Linux)
Direction Générale des Technologies de l'Information et de la Communication
Université de Montréal
PAVILLO
Hi Björn,
Hmm, I guess I should have phrased my question more clearly. What I'm
trying to do is to get Galaxy to satisfy a missing tool dependency at
*tool runtime* using a bioconda package that is only available for
Python3. I am able to satisfy the dependency *manually* by running:
conda c
Hi,
can you check the package? The package should have a dependency on
python3, if not the package seems to be broken :(
Ciao,
Bjoern
Am 03.11.2016 um 21:32 schrieb Wolfgang Maier:
> Hi Björn,
>
> Hmm, I guess I should have phrased my question more clearly. What I'm
> trying to do is to get Gal
I'm not quite sure if I understand you correctly, but let's see.
The original tool wrapper stated
python3
as a dependency. This did not work with at runtime installation at all
because conda cannot resolve python3 and the requirement got ignored by
Galaxy. I changed the requirement tag now to:
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