Re: [galaxy-dev] Job is queued for imported dataset in library

Hello Martin, Thanks for your help. I found that the problem was actually in the job_conf.xml file. Due to a bad configuration it couldn't assign handlers to jobs for uploading data. I used the default file and now everything is fixed. (and it was the master branch of the latest release). So it

Re: [galaxy-dev] "--net None" option in Galaxy (Docker)

Hi Jocelyn, are you referring to the Docker --net option? https://docs.docker.com/engine/userguide/networking/dockernetworks/ If so you can change the --net option during container startup. For example with docker run --net=host -p 8080:80 bgruening/galaxy-stable I'm wondering if there is n

Re: [galaxy-dev] "--net None" option in Galaxy (Docker)

Hi; I think I started a thread on a similar issue on this list. The answer was to configure properly config/job_conf.xml, adding the docker runner and the docker_net param within it to "bridge": true 6G

Re: [galaxy-dev] IE setup problem

Hi Mic, Since you asked for the supervisord config... it would look something like this:] [program:galaxy_proxy] command=/usr/local/bin/node /path/to/galaxy/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 --port 8800 --sessions /path/to/galaxy/database/session_map.sqlite --cookie galaxysession --ver

Re: [galaxy-dev] Job is queued for imported dataset in library

Hi Makis, I am happy to hear that. Thank you for using Galaxy. Martin On Fri, Dec 18, 2015 at 4:03 AM Makis Ladoukakis wrote: > Hello Martin, > > Thanks for your help. I found that the problem was actually in the > job_conf.xml file. Due to a bad configuration it couldn't assign handlers > to

[galaxy-dev] REST API - Tool input information

Is it possible to get tool input information through the REST api? For example, I would like to know for a specific tool to retrieve the inputs needed and the types of inputs being either integer, dataset, string, etc… Kind regards, Jasper Koehorst __

[galaxy-dev] "--net None" option in Galaxy (Docker)

Dear Galaxy team, I'm Jocelyn Brayet, I’m a bioinformatician of Institut Curie (France). I work with Alban Lermine on Galaxy tools development. I currently create tools in Docker for the Galaxy Tool Shed. But, when Galaxy runs Docker, it adds the "—net None" option. The issue is that my tools r

Re: [galaxy-dev] "--net None" option in Galaxy (Docker)

Hi Bjoern and Mikel, Thanks you very much for your feedbacks ! I have corrected my job_conf.xml and it's ok. Thanks Have a nice week end, Jocelyn De : Mikel Egaña Aranguren [mikel.egana.arangu...@gmail.com] Envoyé : vendredi 18 décembre 2015 14:21 À : Bjoern Grue

Re: [galaxy-dev] INIT script for Ubuntu

Hi Mic, I based my startup script on the ones found here: 1. https://wiki.galaxyproject.org/Events/GCC2012/TrainingDay/WS5?highlight=%28init.d%29 2. http://simison.com/brian/GalaxyAdmin_notes.html HTH, Keith > On Dec 17, 2015, at 5:54 PM, Mic wrote: > > Hello, > Where could I find INIT scrip

[galaxy-dev] GCC2016 Web Site is Up: Including registration rates, and full training schedule

Hello all, We are pleased to announce that the *2016 Galaxy Community Conference website is now online * and includes registration information and the full training schedule . GCC2

Re: [galaxy-dev] INIT script for Ubuntu

HI Keith, Thank you for the links. In both links they use *universe_wsgi.ini*, but I am using *galaxy.ini*. Do I have to change to* universe_wsgi.ini *and does it has any advantages over *galaxy.ini*? Thank you in advance. Best wishes, Mic On Sat, Dec 19, 2015 at 1:51 AM, Suderman Keith wrote:

Re: [galaxy-dev] IE setup problem

Hi all, Thank you for the responses. If I would use "dynamic_proxy_manage_proxy=True" than Galaxy would execute automatically: /lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ --cookie galaxysession --verbose without the need to u

Re: [galaxy-dev] IE setup problem

19. des. 2015 1.17 a.m. skrev "Mic" : > > Hi all, > Thank you for the responses. If I would use "dynamic_proxy_manage_proxy=True" than Galaxy would execute automatically: > > /lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ > --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ > --co

Re: [galaxy-dev] IE setup problem

dynamic_proxy_manage_proxy=True is a terrible hack, I would set it to False and use supervisord if you have any inclination to at all. Like sqlite or the local job runner, it is just an attempt to make sure things work out of the box but it isn't that robust. -John On Sat, Dec 19, 2015 at 1:20 AM

[galaxy-dev] IE Apache Proxy config file

Hello, I would like to setup Rstudio and IPython using Apache Proxy. I found the following settings: # IPython specific. Other IEs may require their own routes.ProxyPass /galaxy/gie_proxy/ipython/api/kernels ws://localhost:8800/galaxy/gie_proxy/ipython/api/kernels # Global GIE configurationPr

[galaxy-dev] Rstudio and Ipython supported versions for IE

Hello, Which Rstudio and Jupyter/ipython versions are supported by IE? Thank you in advance. Mic ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists,