Problem with MACS2 Install?

Question

[priyasshah]

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 PYTHONPATH and 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!

[tombills1997]

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.

[Shicheng Guo]

much easier way should be install it using conda:

conda install -c bioconda macs2

if you don't have conda, install conda like this way:

cd /gpfs/home/guosa/hpc/tools
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86_64.sh

[ATpoint]

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.

Answer 1

[priyasshah]

Update, I originally assumed that I needed to set the PYTHONPATH because MACS2 is a python package. I didn't see it automatically added to my PATH, so I added this PATH to my .bash_profile:

export PATH=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin:$PATH

Now the macs2 command works fine! Thanks so much for your input!

Answer 2

[GouthamAtla]

As you are installing with sudo, it should have been already added to PATH. You don't need to set the PATH. and moreover macs2 will not be in site-packages, it will reside in one of the bin directories. Just find out where is the macs2 file residing.

sudo find / -name macs2

[priyasshah]

Thanks for your response, Goutham! I reset my .bash_profile to not execute the .bashrc. And this is what I get when I look at my PATH now:

otp588416ots:~ Priya$ echo $PATH
/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin

otp588416ots:~ Priya$ echo $PYTHONPATH
## *nothing*

Now, when I try to call macs2, I still get the same error. So it seems as though I am still not in the right place when I call macs2:

otp588416ots:~ Priya$ macs2 callpeak -t ChIP.bam -c Control.bam -f BAM -g hs -n test -B -q 0.01
-bash: macs2: command not found

It looks like macs2 could be in several locations (maybe from the multiple install attempts?). This is what I got when I used the find command to locate macs2:

otp588416ots:~ Priya$ sudo find / -name macs2
Password:
find: /dev/fd/3: Not a directory
find: /dev/fd/4: Not a directory
/Library/Python/2.7/site-packages/MACS2-2.1.0.20150731/bin/macs2
/Library/Python/2.7/site-packages/MACS2-2.1.0.20150731/build/scripts-2.7/macs2
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/macs2
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/MACS2-2.1.0.20150731/bin/macs2
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/MACS2-2.1.0.20150731/build/scripts-2.7/macs2

I get the same error when I call macs2 after setting the PYTHONPATH to:

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin

Any additional thoughts?

[priyasshah]

Update, I originally assumed that I needed to set the PYTHONPATH because MACS2 is a PYTHON package. I didn't see it automatically added to my PATH, so I added this PATH to my .bash_profile:

export PATH=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin:$PATH

Now the macs2 command works fine! Thanks so much for your input!

Answer 3

[jimmy_zeng]

## Download and install macs2  
## https://pypi.python.org/pypi/MACS2/

cd ~/biosoft
mkdir macs2 &&  cd macs2
wget  ~~~~~~~~~~~~~~~~~~~~~~MACS2-2.1.1.20160309.tar.gz
tar zxvf MACS2-2.1.1.20160309.tar.gz
cd MACS2-2.1.1.20160309
python setup.py install --user

Then you can use it by: ~/.local/bin/macs2 --help