Hello Philipe,

Is this problem occurring on the public Main Galaxy server at http://main.g2.bx.psu (usegalaxy.org)? If so, please submit a bug report so that we can examine.
http://wiki.g2.bx.psu.edu/Support#Support.Reporting_tool_errors

If this is occurring on a local instance, it could be that there is a mismatch between the version of MACS supported by the Galaxy wrapper and the version of MACS installed. The current wrapper is for MACS v 1.3.
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies

The final possibility is that this is on another public instance - if you need help finding out how to contact their support/administrator, or if your question has been misunderstood, please let us know.

Best,

Jen
Galaxy team

On 10/28/12 5:40 PM, Philipe Moncuquet wrote:
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






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