I'm having trouble setting up the apache to redirect my local running
galaxy which runs on localhost:8080
I would like that people could have access inside the lab knowing my
local ip address. I read plenty of tutorials, can anyone help setting it
up on Ubuntu? The files I have to modify
trying to get my tools going, part 29. I have a Docker image with the latest
Galaxy release, patched to fix the Conda install bug I found earlier, my tools
are installed ok and I’ve added a few from the toolshed for good measure.
One of my tools requires R 3.0.2 which is installed ok.
I read the documentation about conda shared early in this email and I have
one more question:
If I already a conda installation on computer and don't wish share this
installation to control galaxy dependencies, galaxy works fine with your
own conda auto installation or I have pay
No previous instance of reports running, and I'm not sure what to check as
far as ports.
our AWS guy said it might be an issue with AWS but I don't know enough
about all this to confirm (or to know how to confirm).
thanks for your help.
On Thu, Sep 1, 2016 at 1:39 PM, Martin Čech
Cris: maybe check what ports are configured for your Galaxy and/or Tool
Shed to make sure they are not in conflict. I don't know enough about AWS
to help you more, maybe someone else will jump in.
On Thu, Sep 1, 2016 at 1:48 PM Cristel Thomas
> No previous
they migrated the code of e-utils to github. Download path is corrupted:
Please keep all replies on the list by using "reply all"
in your mail client. To manage your
The scatterplot tool is relatively old and has not had its dependencies
updated to be conda compatible.
The relevant lines are these:
> trying to get my
Forgot to paste the link:
On 1 September 2016 at 11:08, Marius van den Beek
> Hi Steve,
> The scatterplot tool is relatively old and has not had its dependencies
> updated to be conda compatible.
I'm not quite sure what you mean by a "code file", but if you
mean using the tag, here's an example:
I am using a Cheetah syntax for loop to access each entry
in a repeat parameter.
On Thu, Sep 1, 2016 at
On Thu, Sep 1, 2016 at 9:36 AM, Katherine Beaulieu <
> Hi Peter,
> The code file tag is generally used in populating select lists. So
> basically you have a function from a code file that is loaded before
> runtime of the tool and you can dynamically load
Hello Galaxy Community,
I was wondering if anyone had ever come across a situation where they have
had to pass the contents of a repeat parameter to a code file in a Galaxy
tool config? Is there any way to do this?
Ah - I understand what you mean now. Using the code tag is
discouraged, but you may find some of these examples useful
for what you are trying to do:
I hope that helps,
On Thu, Sep 1, 2016 at 2:37 PM, Katherine Beaulieu
Today after perform some tests with conda on galaxy 16.07 the follow
message was returned in my terminal:
"*Conda dependency seemingly installed but failed to build job environment.*
The error occurs when *build_isolated_environment()* function is call.
Below some variable values:
I presume you looked at this already:
Those instructions work for Ubuntu as well. What do your Apache2
error logs says (in /var/log/apache2/)? And what have you tried in
your configuration files?
And are you trying to forward
what `host` and `port` is in your reports.ini config file? This stacktrace
would point at something already running at the same port.
On Thu, Sep 1, 2016 at 12:36 PM Cristel Thomas
> Galaxy admins,
> One of you has probably seen the below error
One of you has probably seen the below error before, can someone explain?
for background, we're running our instance on a AWS server (if that makes a
galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,545 Enabling
'sample_tracking' controller, class: SampleTracking
the config is:
port = 8081
host = 0.0.0.0
this is the first time we have that issue though, and the instance has been
running just fine until now. I don't think we've changed anything.
On Thu, Sep 1, 2016 at 12:40 PM, Martin Čech wrote:
> Hi Cris,
> what `host`
Cris: please check whether some previous instance of Reports isn't still
running and/or check your ports using e.g. `netstat`
On Thu, Sep 1, 2016 at 1:19 PM Cristel Thomas
> Hi Martin,
> the config is:
> port = 8081
> host = 0.0.0.0
> this is the first time
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