[galaxy-dev] GCC2015 Training Day Topic Voting is open. Please vote!

Hello all,What topics should be offered at the GCC2015 Training Day ? Topics for the GCC2015 Training Day are selected by you, the Galaxy Community. There are nominated topics

Re: [galaxy-dev] Unable to connect galaxy server after upgrade to latest version

No clue what is wrong - hopefully you figured this out. If you haven't, can you send us your Galaxy log file for the web server loading - you can send it to me personally and galaxy-b...@bx.psu.edu - if you are worried about disclosing private information on the public list? Also it would be inte

Re: [galaxy-dev] Manually adding new tools from toolshed

I am skeptical that setting up a local tool shed is worth the effort - it seems like overkill. I think just downloading the tar balls, manually modifying the datatypes_conf.xml is fine. If you set the tool_dependencies_dir in your Galaxy configuration - you can also create a isolated environments

Re: [galaxy-dev] EOF error with tool

There are a couple groups working on improved trinity wrappers - I don't think they have reach the tool sheds though :(. As for the details of your specific tool - I think I would really need to see the tool to guess at the issue. Would it be possible to send us the problematic tool XML file or pa

Re: [galaxy-dev] galaxy and torque - resource allocation

Galaxy generally defers to the DRM (torque in your case) for dealing with these things. In your job_conf.xml you can specify limits for memory or CPUs and Galaxy will pass these along to the DRM at which point it is up to the DRM to enforce these - details depend on if you are using the PBS runner

Re: [galaxy-dev] FastQC wrapper not seeing files at gzipped

Peter has already voted and if I recall correctly Ryan cannot access Trello - so this might be a waste to bring up - but here is a Trello card for voting on this issue and tracking progress https://trello.com/c/3RkTDnIn. To summarize previous discussion - this would be fantastic to have and Galaxy

Re: [galaxy-dev] Getting 'No space left on device' at testtoolshed

Thanks for the bug report. This has been resolved for now - but it does seem to happen more than it should. There should ideally be nagios checks in place to make warn us before it gets to this point - I will try to ask around about that. -John On Mon, Jan 12, 2015 at 6:18 PM, Jeltje van Baren

Re: [galaxy-dev] Display of file content in a combobox

I don't know how to do this exactly - but I think it is possible with a custom datatype. I think you define a custom datatype (you will probably want to extend the Galaxy tabular datatype), then I believe you will need to override the set_meta method on the datatype to collect a new metadata field

Re: [galaxy-dev] Create a package with binaries

Yes, I think this is the current best practice pattern - where you would stick the first tool_dependencies.xml in a "Tool Dependency Definition" repository named package_ballast_1_0 and the the other tool_dependencies.xml file would just sit in the tool_dependencies.xml file corresponding to say an

Re: [galaxy-dev] Partial automation for generating those twisty R dependency tool shed installation sequences

Hi Ross, Am 13.01.2015 um 00:13 schrieb Ross: > Hi Björn, > I'm a bit old fashioned and think I prefer a proper Galaxy tool rather than > a notebook :) :) > So I've set up a temporary demonstration/test site of a > toolfactory generated tool that does what I think I need - can some kind > soul