...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.m...@gmail.com>
To:     <galaxy-u...@lists.bx.psu.edu>


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 ?


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