MACS failed because of lambdaset options
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 ( <param name="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
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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