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

2014-03-27 Thread Assaf Gordon
Hello Galaxy People! (it's been a while since I've last been here... a pleasure to be back). I intend to publish a small command-line utility, which will also be available through Galaxy Toolshed. It'll be a small application note, so not a lot of space for many citations. The relevant

Re: [galaxy-dev] Errors loading data into IGV from Galaxy

2014-03-27 Thread Hillman, Paul R.
Dear John and the Galaxy team, Thank you for your prompt response however, I am still getting the same error that I reported previously. I attempted to load the data again at 9:45am Central Time on Wednesday March 26th, and received the following error Errors were encountered loading the

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

2014-03-27 Thread tima
Hi Guys, is it possible to add E.coli K12 genome for mapping with Bowtie on Andromeda-NCBI portal? thanks, timur ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and

Re: [galaxy-dev] trackster is not working on the vrelease_2014.02.10--2--29ce93a13ac7

2014-03-27 Thread Shu-Yi Su
Hi Jeremy, I cleaned the catche on both safari and firefox, but it doesn't work. It still shows the same error messages. Thank you very much for the help!! Best, Shu-Yi On Mar 26, 2014, at 2:00 PM, Jeremy Goecks wrote: This sounds like a cache issue. Both of these scripts have been removed

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

2014-03-27 Thread Geert Vandeweyer
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

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

2014-03-27 Thread Janaki Rama Rao Gollapudi
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] How to write test cases for custom tool

2014-03-27 Thread Janaki Rama Rao Gollapudi
Hi, I found below resources: - Running testhttps://wiki.galaxyproject.org/Admin/RunningTests?action=showredirect=Admin%2FRunning+Tests - Writing Functional testshttps://wiki.galaxyproject.org/Admin/Tools/Writing%20Tests Thanks, JanakiRam On Thu, Mar 27, 2014 at 2:53 PM, Janaki Rama

[galaxy-dev] ERROR executing tool

2014-03-27 Thread virginia dalla via
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

2014-03-27 Thread Janaki Rama Rao Gollapudi
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. . tests test param name=input1 value=some string/ param name=input2 value=expected format/ output name=output

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

2014-03-27 Thread Greg Von Kuster
As Janaki replied below, see: http://wiki.galaxyproject.org/Admin/RunningTests?action=showredirect=Admin%2FRunning+Tests On Mar 27, 2014, at 7:15 AM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I have added tests to tool dependency xml, but how should I

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

2014-03-27 Thread Janaki Rama Rao Gollapudi
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

2014-03-27 Thread Greg Von Kuster
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

2014-03-27 Thread Janaki Rama Rao Gollapudi
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 g...@bx.psu.edu wrote: Hello Janaki, Thanks for clarifying that you have installed your tools from a Tool Shed. In this case,

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

2014-03-27 Thread Martin Čech
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, t...@caltech.edu wrote: Hi Guys, is it possible to add E.coli K12 genome for mapping with

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

2014-03-27 Thread James Taylor
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 agor...@wi.mit.edu wrote: Hello Galaxy People! (it's been a while since I've last been here... a pleasure to be