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: