[galaxy-dev] Login reguried causing nested main page loading

Hi All, I tried to turn on login required in config.ini But now if you are not logged in it loads the main page where normally the welcome.html would go. Which then recursively loads other main pages. Which file am I missing? Thanks Christian University of Manchester

Re: [galaxy-dev] Login reguried causing nested main page loading

Hi, Christian and Ryan Which versions of Galaxy are you using when this happens? Thanks, Carl On Mon, Jan 11, 2016 at 9:03 AM, Ryan G wrote: > I've seen this as well. I find that restarting galaxy fixes the problem > but I'd love to know the underlying cause. >

Re: [galaxy-dev] A Report Calc tool which provides a scripting language and interpreter for text mining and quality control

Hi, Thanks for quick reply, and good point about keeping math expressions familiar to most users. In this first round I settled for a simple prefix "function(parameter1 parameter2 ...)". All the python infix operators like "a + b" have equivalent prefix functions "add(a b)" so the latter are

Re: [galaxy-dev] A Report Calc tool which provides a scripting language and interpreter for text mining and quality control

> Yes, infix "a + b" parsing would be easier to read If you are targeting non-programmers, I think the bigger point is that a + b is easier to write. I do understand the motivation for prefix from the implementation standpoint. The issue, I suppose, will be how early you want to include

[galaxy-dev] Job metrics configuration

Hi there I'm trying to understand how the job metrics configuration works. Reading through various examples, it looks like it works together with the dynamic destination support. First on the dynamic destination support, this works, as I understand it, by importing modules (files ending in .py)

Re: [galaxy-dev] running in job_working_directory

To answer my own questions, apparently I missed the outputs_to_working_directory setting in config/galaxy.ini. cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden > On 29 Dec 2015, at 14:04, Jorrit Boekel wrote: >

Re: [galaxy-dev] Login reguried causing nested main page loading

I've seen this as well. I find that restarting galaxy fixes the problem but I'd love to know the underlying cause. Please excuse any typos -- Sent from my iPhone > On Jan 11, 2016, at 5:08 AM, Christian Brenninkmeijer > wrote: > > Hi All, > > I

[galaxy-dev] tools to reduce list of datasets.

Hi All, Can someone point me to documentations/ examples of how to write a tool to reduce a a list of datasets back into a single dataset. == What I want to do is process multiple pairs of reads. 1. load all the fastq files. 2. create a list of pairs 3. Run tools of each pair in the list

Re: [galaxy-dev] Job metrics configuration

Hi there John Thanks for the clarification. My initial aim was, exactly, to expose those parameters that, as you say, some people don't think should be exposed. My use case is to allow jobs with different native parameters to be scheduled on our clouster from our Galaxy server. Perhaps a better

Re: [galaxy-dev] A Report Calc tool which provides a scripting language and interpreter for text mining and quality control

On Jan 11, 2016, at 2:42 PM, Dooley, Damion wrote: > ... we're testing out a basic scripting language ... meant to provide [folks] > with > ways to [do something] without having to be programmers ... > > if( lt(/N50 20) set(report/job/status FAIL)) > > Math is accomplished by python

[galaxy-dev] A Report Calc tool which provides a scripting language and interpreter for text mining and quality control

Folks, we're testing out a basic scripting language and interpreter for report writing and quality control that is meant to provide both command-line programmers and Galaxy platform researchers and admins with ways to tweak workflow quality control behaviour without having to be programmers