Thank Dan, that's what I thought.
So databases can added to any of the multiple blastdb.loc
files which Galaxy ought to be combining. I'm not sure what
went wrong for Harry (and therefore how to avoid it for
others in future). :(
(Separately I have raised the issue of returning the BLAST
datatype
I have galaxy server 15.10 running on Ubuntu 14.04, which has python 2.7.5.
I was in the process of adding matplotlib from the toolchest. It has a
dependency on package_python_2_7.
Before proceeding, I'd like to understand a bit how that works. Does that
install a whole new python, and how then d
Hi Tony,
Yes, Galaxy will install a whole functional python version.
At runtime, Galaxy source some env.sh files according to the different
requirements and the bunch of requirement dependencies.
Using the tool_dependencies, indeed, Galaxy sets almost a dedicated environment
for the tools.
The
I forgot to say that Galaxy installs those dependencies (tool_dependencies or
conda) beside your host system.
That will not interfere with your host libraries, binaries ...
Gildas
-
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Hi all - We are using a SSO system so that user's authenticate externally
from Galaxy.
when I impersonate a user then try to log out as that user, I'm unable to.
I get the page "
Access to Galaxy user controls is disabled
User controls are disabled when Galaxy is configured for external
authentic
Hey, thanks for this. I've made an issue (
https://github.com/galaxyproject/galaxy/issues/2671) and will check it out
today.
On Wed, Jul 27, 2016 at 12:44 PM Ryan G wrote:
> Hi all - We are using a SSO system so that user's authenticate externally
> from Galaxy.
>
> when I impersonate a user t
Thanks. Clearing out the browser history resolved it but there should be a
better way...
On Wed, Jul 27, 2016 at 12:48 PM, Dannon Baker
wrote:
> Hey, thanks for this. I've made an issue (
> https://github.com/galaxyproject/galaxy/issues/2671) and will check it
> out today.
>
> On Wed, Jul 27,
Hello Galaxy Community,
Does anyone know what file would be responsible for creating the info page
after the execution of a tool? This is the page you access after output has
been created in the history, by clicking on the little 'i' icon.
Thanks!
___
Hi Katherine,
That'd be this method:
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/controllers/dataset.py#L978
Which fills this template:
https://github.com/galaxyproject/galaxy/blob/dev/templates/show_params.mako
On Wed, Jul 27, 2016 at 1:20 PM Katherine Beaulieu <
k
Wow thanks for such a quick response!
On Wed, Jul 27, 2016 at 1:22 PM, Dannon Baker
wrote:
> Hi Katherine,
>
> That'd be this method:
> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/controllers/dataset.py#L978
> Which fills this template:
> https://github.com/galaxyp
Hi all,
I ran into a weird behavior on my local instance of galaxy and I was
wondering if anyone had the same experience (and if so what did you do to
fix it?).
When trying to run a workflow by clicking on the workflow name, it works.
When trying to run the workflow by clicking on the arrow next t
Hi again,
I’m looking for the right way to store some user credentials in the galaxy
session so that tools can work on behalf of the user with our repository.
Currently users have an API key and they need to upload it as a data item to
that is then passed to each tool that needs it as input.
This is indeed weird behavior. What revision is your Galaxy at?
On Wed, Jul 27, 2016 at 9:07 PM Cristel Thomas
wrote:
> Hi all,
> I ran into a weird behavior on my local instance of galaxy and I was
> wondering if anyone had the same experience (and if so what did you do to
> fix it?).
>
> When
Hi Anthony,
On Wed, Jul 27, 2016 at 11:16 PM, Tony Schreiner
wrote:
> I have galaxy server 15.10 running on Ubuntu 14.04, which has python 2.7.5.
>
> I was in the process of adding matplotlib from the toolchest. It has a
> dependency on package_python_2_7.
>
> Before proceeding, I'd like to unde
I remember this issue and that it was fixed. Updating to a newer revision
should resolve it.
On Wed, Jul 27, 2016 at 10:06 PM, Dannon Baker
wrote:
> This is indeed weird behavior. What revision is your Galaxy at?
>
> On Wed, Jul 27, 2016 at 9:07 PM Cristel Thomas
> wrote:
>
>> Hi all,
>> I ran
Yep, thought it was familiar and that we'd fixed it. Cristel, let us know
if you have trouble with upgrading -- I just confirmed that this isn't an
issue in the current 16.04 release or on the dev branch.
On Wed, Jul 27, 2016 at 10:27 PM Aysam Guerler
wrote:
> I remember this issue and that it
I did a bit of digging here, and it looks to me like /user/logout should be
whitelisted in the middleware, and shouldn't present that "Access to Galaxy
user controls is disabled".
I might need a little more information. What revision of Galaxy are you
running? Are you serving Galaxy at a subdoma
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