[galaxy-dev] apache on ubuntu

Hi, 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

[galaxy-dev] Conda: confused dependencies with multiple R versions and rpy

Hi, 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.

Re: [galaxy-dev] Introducing Conda as a new standard for Galaxy tool dependencies

Hi Bjorn, 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

Re: [galaxy-dev] error on startup

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

Re: [galaxy-dev] error on startup

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. M. On Thu, Sep 1, 2016 at 1:48 PM Cristel Thomas wrote: > No previous

[galaxy-dev] bug in fastqmcf

Hi they migrated the code of e-utils to github. Download path is corrupted: https://expressionanalysis.github.io/ea-utils/ Cheers Jochen ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your

Re: [galaxy-dev] Conda: confused dependencies with multiple R versions and rpy

Hi Steve, The scatterplot tool is relatively old and has not had its dependencies updated to be conda compatible. https://github.com/galaxyproject/tools-devteam/blob/master/tools/scatterplot/scatterplot.xml The relevant lines are these: numpy rpy wrote: > Hi, > trying to get my

Re: [galaxy-dev] Conda: confused dependencies with multiple R versions and rpy

Forgot to paste the link: https://github.com/galaxyproject/tools-devteam/issues/385 On 1 September 2016 at 11:08, Marius van den Beek wrote: > Hi Steve, > > The scatterplot tool is relatively old and has not had its dependencies > updated to be conda compatible. >

Re: [galaxy-dev] Send repeat parameter to code file for multiple select list

I'm not quite sure what you mean by a "code file", but if you mean using the tag, here's an example: https://github.com/peterjc/galaxy_mira/blob/master/tools/mira4_0/mira4_de_novo.xml I am using a Cheetah syntax for loop to access each entry in a repeat parameter. Peter On Thu, Sep 1, 2016 at

Re: [galaxy-dev] Send repeat parameter to code file for multiple select list

On Thu, Sep 1, 2016 at 9:36 AM, Katherine Beaulieu < katherine.beaulieu...@gmail.com> wrote: > 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

[galaxy-dev] Send repeat parameter to code file for multiple select list

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? Katherine ___ Please keep

Re: [galaxy-dev] Send repeat parameter to code file for multiple select list

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: https://github.com/galaxyproject/galaxy/issues/2714 I hope that helps, Peter On Thu, Sep 1, 2016 at 2:37 PM, Katherine Beaulieu

[galaxy-dev] Problem with conda on galaxy 16.07

Hi folks, 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:

Re: [galaxy-dev] apache on ubuntu

Hi Jochen, I presume you looked at this already: https://wiki.galaxyproject.org/Admin/Config/ApacheProxy 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

Re: [galaxy-dev] error on startup

Hi Cris, what `host` and `port` is in your reports.ini config file? This stacktrace would point at something already running at the same port. Martin On Thu, Sep 1, 2016 at 12:36 PM Cristel Thomas wrote: > Galaxy admins, > One of you has probably seen the below error

[galaxy-dev] error on startup

Galaxy admins, 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 difference) galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,545 Enabling 'sample_tracking' controller, class: SampleTracking

Re: [galaxy-dev] error on startup

Hi Martin, 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`

Re: [galaxy-dev] error on startup

Cris: please check whether some previous instance of Reports isn't still running and/or check your ports using e.g. `netstat` M. On Thu, Sep 1, 2016 at 1:19 PM Cristel Thomas wrote: > Hi Martin, > the config is: > port = 8081 > host = 0.0.0.0 > > this is the first time