Re: [galaxy-dev] Citing Galaxy + Toolshed in an app note of a small tool

Hey Assaf, For Cite1 (Galaxy): doi:10.1186/gb-2010-11-8-r86 For Cite2 (ToolShed): doi:10.1186/gb4161 Thanks for asking! -- jt On Tue, Mar 25, 2014 at 1:15 PM, Assaf Gordon wrote: > Hello Galaxy People! > > (it's been a while since I've last been here... a pleasure to be back). > > I intend t

Re: [galaxy-dev] adding E.coli K-12 genome for mapping

Hi, I added your request to the card where we track these: https://trello.com/c/mJWnAuuQ/1511-to-request-reference-genome-comment-on-this-card Martin Galaxy team On Wed, Mar 26, 2014 at 3:17 PM, wrote: > Hi Guys, > > > is it possible to add E.coli K12 genome for mapping with Bowtie on > Andro

Re: [galaxy-dev] How to write test cases for custom tool

Thank you, I will go through the resources and will reply my results to this email chain. Thanks, JanakiRam On Thu, Mar 27, 2014 at 6:39 PM, Greg Von Kuster wrote: > Hello Janaki, > > Thanks for clarifying that you have installed your tools from a Tool Shed. > In this case, functional tests d

Re: [galaxy-dev] How to write test cases for custom tool

Hello Janaki, Thanks for clarifying that you have installed your tools from a Tool Shed. In this case, functional tests do not use Galaxy's tool_conf.xml.sample, so changing it will make no difference. For information about running functional tests on tools installed from the Tool Shed, see:

Re: [galaxy-dev] How to write test cases for custom tool

Hi, Thanks for reply. I composed a details email for better clarity. when run grep command in galaxy home folder ( ./run_functional_tests.sh -list | grep barcode-parse), I got no results. What I did was: - Implemented a custom tool (It has one python script and tool definition file. These

Re: [galaxy-dev] How to write test cases for custom tool

As Janaki replied below, see: http://wiki.galaxyproject.org/Admin/RunningTests?action=show&redirect=Admin%2FRunning+Tests On Mar 27, 2014, at 7:15 AM, Janaki Rama Rao Gollapudi wrote: > Hi, > > I have added tests to tool dependency xml, but how should I run these tests, > can you please help

Re: [galaxy-dev] How to write test cases for custom tool

Hi, I have added tests to tool dependency xml, but how should I run these tests, can you please help me to run test cases. . .. Thanks, G.JanakiRam On Thu, Mar 27, 2014 at 3:27 PM, Janaki Rama Rao G

[galaxy-dev] ERROR executing tool

Hi, I tried to GROOMER my fastq data in fastq data, and galaxy did not allowed me:Error executing tool: objectstore, __call_method failed: get_filename on , kwargs: {}could you please help me?Thank you viR

Re: [galaxy-dev] How to write test cases for custom tool

Hi, I found below resources: - Running test - Writing Functional tests Thanks, JanakiRam On Thu, Mar 27, 2014 at 2:53 PM, Janaki Ra

[galaxy-dev] How to write test cases for custom tool

Hi, I have implemented a custom tool which will parse a given string in to expected format. Installed this custom tool into galaxy and was able to run successfully. I would like to add test cases to this tool, can you please provide me resources to write test cases for this custom tool. Is this

Re: [galaxy-dev] Galaxy startup takes very long. Normal?

I'm using galxy-dist. That's why I don't have the setting. Thanks for the information, I'll wait for the next stable release and update the settings then. Geert On 03/26/2014 01:59 PM, Greg Von Kuster wrote: The changeset that made this a configurable setting was committed to the stable branc