[galaxy-dev] tool problems (data_manager_fetch_ncbi_taxonomy & ggplot2)

Dear mailing list, I'm experimenting with the tools available at the Tool Shed and ran into problems with two of the tools. 1. data_manager_fetch_ncbi_taxonomy If I run the data manager I get an error in the browser: "Uncaught exception in exposed API method" The terminal shows the

Re: [galaxy-dev] Rg: Galaxy Version

Thanks Martin & Eugen, That's much easier (although Anamika will likely need to check if their Galaxy was setup using hg or git anyway for updating it). I'm not sure when it was introduced, but its been a while as even the older Galaxy instance in my example under hg gives: {"version_major":

Re: [galaxy-dev] Search Tool Shed

Hi Matthias, it is supposed to open an iframe in the right panel with view of MTS categories for browsing. Do you see a warning icon in the right of your browser's URL bar? I think I saw this before when there was https/https mismatch. How does your config/tool_sheds_conf.xml look like? Do you

[galaxy-dev] Search Tool Shed

Dear mailing list, What is the expected behavior if I click in the Admin area under "Search Tool Shed" on the "Galaxy Main Tool Shed" button (or any of the Browse .. or Search .. actions that are available via the black triangle submenu)? I remember that a new tab with the corresponding Tool

Re: [galaxy-dev] Shared Data Library, large number of files

Can you please share your '/client/galaxy/scripts/layout/menu.js' file with me? (e.g. using https://gist.github.com or similar). thanks M. On Wed, Mar 8, 2017 at 1:34 PM D K wrote: > Hi Martin, > > I've tried this on both v16.07 and v16.10 > > D > > > > On Wed, Mar

[galaxy-dev] Fwd: [Bosc] BOSC 2017: Call for Abstracts

Dear all, Recent BOSC meetings have had a strong Galaxy presence, so please do consider submitting an abstract and/or attending BOSC 2017 in Prague. Thank you, Peter Dr. Peter Cock, Bioinformatician at The James Hutton Institute; Open Bioinformatics Foundation, board of directors, treasurer;

Re: [galaxy-dev] Shared Data Library, large number of files

Daniel: what version is your Galaxy? Martin On Wed, Mar 8, 2017 at 12:40 PM D K wrote: > I've copied and pasted the javascript error below. Any help would be > greatly appreciated. Thanks! > > Uncaught TypeError: Cannot read property 'masthead' of undefined > at

Re: [galaxy-dev] Rg: Galaxy Version

Check lib/galaxy/version.py Bests, Haiqing From: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] On Behalf Of Anamika Singh Sent: Wednesday, March 08, 2017 2:37 AM To: galaxy-dev@lists.galaxyproject.org Subject: [galaxy-dev] Rg: Galaxy Version Dear galaxy team, I am using

Re: [galaxy-dev] Shared Data Library, large number of files

I've copied and pasted the javascript error below. Any help would be greatly appreciated. Thanks! Uncaught TypeError: Cannot read property 'masthead' of undefined > at n. (menu.js:120) > at Function.each (jquery.js:370) > at HTMLDocument. (menu.js:117) > at l (jquery.js:3232) >

[galaxy-dev] DeepTools installation error

Hi all, trying to install the deeptools_suite from the toolshed I only get the following error: "500 Internal Server Error nginx/1.11.10" This happens as well for the dependencies, e.g. deeptools_bigwig_compare. I am currently using Galaxy 16.10 with nginx proxy. Also the installation of the

Re: [galaxy-dev] Shared Data Library, large number of files

Hi Martin, I've pasted the file you requested here: http://collabedit.com/xcx5b Thanks! On Wed, Mar 8, 2017 at 11:04 AM, Martin Čech wrote: > Can you please share your '/client/galaxy/scripts/layout/menu.js' file > with me? (e.g. using https://gist.github.com or similar).

Re: [galaxy-dev] DeepTools installation error

The documentation here is quite good: https://docs.galaxyproject.org/en/master/admin/conda_faq.html As an aside, the dockerized version of Galaxy (https://github.com/bgruening/docker-galaxy-stable) from Björn Gruening makes this convenient. Devon On 03/08/2017 08:55 PM, Md. Rezaul Karim

Re: [galaxy-dev] DeepTools installation error

Hi Timo, Use conda for dependency resolution in Galaxy and make your life easier :) Devon On 03/08/2017 06:31 PM, Timo Janßen wrote: Hi all, trying to install the deeptools_suite from the toolshed I only get the following error: "500 Internal Server Error nginx/1.11.10" This happens as

Re: [galaxy-dev] DeepTools installation error

Hi Devon, I'm also experiencing similar issues. Could you please briefly explain how to use Condo with Galaxy? Is there any other versions where Conda is integrated apart from the regular Galaxy distributions? On Mar 8, 2017 7:38 PM, "Devon Ryan" wrote: > Hi Timo, > > Use

Re: [galaxy-dev] Shared Data Library, large number of files

The code at L120 does not exist in 16.07. It was broken in 16.10 and fixed for 17.01. I made a PR to backport the fix to 16.10: https://github.com/galaxyproject/galaxy/pull/3728 You shouldn't be seeing the 'Cannot read property 'masthead' of undefined' error in 16.07 and it should be fixed in

Re: [galaxy-dev] Rg: Galaxy Version

Dear Anamika, you can check the version in your browser using the link $link_to_your_galaxy/api/version. Example for the usegalaxy.org: https://usegalaxy.org/api/version Best, Eugen On 08 Mar 2017, at 11:36, Anamika Singh

[galaxy-dev] Rg: Galaxy Version

Dear galaxy team, I am using galaxy platform (old version) in Linux OS which was not installed by me. I would like to know 'how to check what is the galaxy version installed currently in my system. Regards -- Anamika ___ Please keep all