The wrapper you are using is for MACS 1.3, there is a wrapper that is
compatible with 1.4 in the toolshed.

--
James Taylor, Assistant Professor, Biology/CS, Emory University


On Fri, Feb 15, 2013 at 9:26 AM, greg <margeem...@gmail.com> wrote:
> Hi guys,
>
> I'm trying to run MACS in my local galaxy install (see screenshot:
> http://snag.gy/5QGUH.jpg)
>
> And I'm getting this error:
>
> 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
>
> Thanks in advance for any help.
>
> -Greg
>
> Here's how I installed Macs (I guess it doesn't come built in?)
>
>> cd /usr/local/galaxy/downloads/
>> wget https://github.com/downloads/taoliu/MACS/MACS-1.4.2-1.tar.gz
>> tar -xzvf MACS-1.4.2-1.tar.gz
>> cd MACS-1.4.2
>> source /usr/local/galaxy/job_environment_setup_file
>> python setup.py install
>> deactivate
>> cd /misc/local/galaxy/galaxy_python/bin
>> ln -s macs14 macs
>
> (and made sure /misc/local/galaxy/galaxy_python/bin is on the galaxy
> user's path)
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