I have Python (2.7.10) on my Mac. I installed MACS2 for ChIP-seq peak calling. However I think my install is not complete or my PYTHONPATH is not point to the correct place. When I try to call macs2 I get the following error:
otp588935ots:~ Priya$ macs2 callpeak -t ChIP.bam -c Control.bam -f BAM -g hs -n test -B -q 0.01 -bash: macs2: command not found
I have set my
PATH to these values in my .bashrc:
export PYTHONPATH=/Library/Python/2.7/site-packages:$PYTHONPATH export PATH=/bin:$PATH
When I try repeating the install (using pip or from source code) I find that it is already installed in the following location:
otp588935ots:~ Priya$ sudo -H pip install MACS2 Requirement already satisfied (use --upgrade to upgrade): MACS2 in /Library/Python/2.7/site-packages Requirement already satisfied (use --upgrade to upgrade): numpy>=1.6 in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from MACS2)
Am I pointing to the wrong PATH/PYTHONPATH? Any thoughts would be greatly appreciated! Thank you!
Try reinstalling the whole program, I am quite sure that this issue will be resolved, however, while installing I came up with an unknown error called Mac Error Code 43, any solution regarding this issue will be appreciated.
much easier way should be install it using conda:
if you don't have conda, install conda like this way:
Will move to comment as 1) issue is solved > 3 years back, 2) OP was using Mac not Linux and 3) OP was asking specifically about a PYTHONPATH issue, but not conda. You are posting absolute paths that are specific to your computer (here and in multiple previous posts including some tutorial-like posts), there is little use in doing that. Shicheng Guo you are a very experienced user and good input is always appreciated, but please be smarter about your posts.