Re: [galaxy-user] Illumina Methylation tool in toolshed

Hi Sachit, not in the toolshed but you can find a start here: https://github.com/bgruening/galaxytools/tree/master/illumina_methylation_analyser its for the 450k chips, I have also some tools for WGMA if you are interested. Cheers, Bjoern > Hi, > > This is my third post regarding this matter

Re: [galaxy-user] Illumina Methylation tool in toolshed

tool shed or in > github? > > Thanks, > > Sachit > > > On Mon, Jul 29, 2013 at 2:53 PM, Bjoern Gruening < > bjoern.gruen...@pharmazie.uni-freiburg.de> wrote: > > > > > Hi Sachit, > > > > not in the toolshed but you can f

Re: [galaxy-user] (no subject)

Hi Meabh, I'm not familiar with such tools, but maybe you can merge the original files with read-count back to your result file -> "Join two Datasets side by side on a specified field". Cheers, Bjoern > I am new to Galaxy and am using it for analysis of BLAST results and > phylogeny. I have upl

[galaxy-user] Join the HOMER Galaxy wrapper development!

Hi Galaxy Tool developers! I have started to integrate the HOMER suite into Galaxy. My initial attempt can be found here: https://github.com/bgruening/galaxytools/tree/master/homer Currently, we make use of: - Tool Shed definitions of all required 3rd Party Software - datatype definitions - loc

Re: [galaxy-user] Is anyone using Galaxy with NeuroScience ?

Hi Zeeshan, there was a nice poster @GCC2013. http://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Events.2FGCC2013.2FAbstracts.2FPosters.P2:_Cloud-based_Image_Analysis_and_Processing_Toolbox Cheers, Bjoern > Hi, Is any one using galaxy for Neuroscience and brain imaging ? > > > -- > >

Re: [galaxy-user] Galaxy Tool Version Question

Hi Scott, please click on the 'i' info icon in one of your datasets (next to the download button) you will find many additional information's, including the wrapper version and the version of the underlying tool. Cheers, Bjoern > To Whom it May Concern, > > > I was trying to find the version

Re: [galaxy-user] About tool classify in the tool box panel

Hi Xiao, have a look in your tool_conf.xml file. You can specify sections with the section tag. Keep in mind that the ID needs to be unique. Cheers, Bjoern > Dear all > > > I want to know how to part the tool panel into several group just like > the public Galaxy. It cla

Re: [galaxy-user] Fwd: About empty no peek problem

Hi Xiao, the attached ones are working for me, hope for you too. Cheers, Bjoern > Dear Bjorn > > > The configure xml file and the relevant R scripts is attached. > > > Thank you for all your help. > > > Regards, > XiaoTao > The University of HongKong > > > 2013/9/3 Björn Grüning >

Re: [galaxy-user] Fwd: About empty no peek problem

terpreter. Its recommended to use the "${}" notation. You never know if your path to input or output has some white spaces or other pitfalls included. Ciao! Bjoern > > Cheers! > Xiaotao > > > 2013/9/3 Bjoern Gruening > Hi Xiao, > > the attac

Re: [galaxy-user] problem running Augustus

Hi Claudio, I will have a look at it, at latest tomorrow, promised. Cheers, Bjoern (Augustus wrapper developer) > > > I am trying to use the genome Annotation tool Augustus on my locally > installed copy of Galaxy. After loading the data file, all analyses > stop and deliver the following: >

Re: [galaxy-user] error:ordinary output of macs in stderr

Hi Han, you can filter the output of every tool and react on it with the stdio tag in Galaxy. for more information please have a look at the wiki page: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cstdio.3E.2C_.3Cregex.3E.2C_and_.3Cexit_code.3E_tag_sets Cheers, Bjoern > Hello,