On Feb 15, 2013 9:37 AM, "greg" <margeemail@gmail.com> wrote:

Thanks!  So one question, when I go to install it from the toolshed I
see two choices for a revision to select:

3:cdd9791c0afa
0:c1eeccec29d1

Which would I choose and why?

Thanks,

Greg

On Fri, Feb 15, 2013 at 9:30 AM, James Taylor <james@jamestaylor.org> wrote:
> 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 <margeemail@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)
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
>>   http://lists.bx.psu.edu/