...moved to dalaxy-dev, since it is about your local Galaxy instances:

Hi Philippe

Your galaxy wrapper for MACS expects version 1.3, where the option "--lambdaset" is present. (see https://github.com/taoliu/MACS/blob/macs_v1/ChangeLog)

Regards, Hans-Rudolf

-------- Original Message -------- Subject: [galaxy-user] MACS failed because of lambdaset options Date: Mon, 29 Oct 2012 11:40:28 +1100 From: Philipe Moncuquet philippe.mcqt@gmail.com To: galaxy-user@lists.bx.psu.edu

Hi,

I am trying to use MACS and I get the following error when the job fails :

Usage: macs <-t tfile> [-n name] [-g genomesize] [options]

Example: macs -t ChIP.bam -c Control.bam -f BAM -g h -n test -w --call-subpeaks

macs: error: no such option: --lambdaset

I am not really familiar to MACS so I checked the documentation and it seems Galaxy is rigth to complain because there is no such option as --lambdaset (http://liulab.dfci.harvard.edu/MACS/README.html). I went back to the xml wrapper and there is this ( <paramname="lambdaset"type="text" ....) parameters that corresponds to the text box

3 levels of regions around the peak region to calculate the maximum lambda as local lambda:

Does anyone face the same problem ? Any clue on what I should try, should I modify the wrapper ?

Cheers, Philippe