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macs2 conda installation problem

Hi,

I am trying to install Macs2 on my Mac using bioconda. However I get the following error:

Solving environment: failed

UnsatisfiableError: The following specifications were found to be in conflict:

  • macs2 -> python[version='>=2.7,<2.8.0a0'] -> *[track_features=debug]
  • python=3

Use "conda info <package>" to see the dependencies for each package.

I have both Python 2.7 and Python3 on my computer. Seems that maybe condo is seeing Python3, then refusing to install since Macs2 only works with Python 2.7. Anyone know if this is something I can fix by changing PATH to Python, or somehow making Python2.7 the default that condo sees?

Thanks,

software error python version macs2 osx
• 9,241 views • link
updated by h.mon h.mon • written by jcs92 • jcs92

On my linux(ubuntu 16.04) I usually change the defualt python version by adding 

alias python='python2'

this line at the start of .bashrc file present in the home directory.

And if I want to use the syatem's python instead of conda, I will change the $PATH variable added by conda from

export PATH=/home/anaconda/bin/:$PATH

To

export PATH=$PATH:/home/anaconda/bin/

In .bashrc file.

• 1 views • link
written by Nitin Narwade Nitin Narwade

Thanks for replying, but modifying the bash file didn't work.

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written by jcs92 • jcs92

I think you need to source the .bashrc file after adding those lines or you can simply restart the session(terminal).

And one more tip just run 

which python2
commamd and set the PYTHONPATH variable as mentioned here

Thank you.

• 1 views • link
written by Nitin Narwade Nitin Narwade

PYTHONPATH is no longer relevant when installing via conda

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written by Joe Joe

3 answers

You can use conda to create a virtual environment with the appropriate python version.

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written by WouterDeCoster WouterDeCoster

It is unadvisable to manipulate system python binaries (particularly on Mac), so Wouter’s answer is absolutely the way to go.

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written by Joe Joe

Worked Wouter! Thanks!

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written by jcs92 • jcs92

sudo pip install MACS2 This should be able to install macs2. Please update following before trying:

1) pip install --upgrade pip 2) pip install numpy 3) pip install --upgrade numpy

Cheers !!

• 1 views • link
written by Praneet Chaturvedi Praneet Chaturvedi

That was going smoothly until I got this error:

Command "python setup.py egg_info" failed with error code 1 in /private/tmp/pip-install-zj61p_t2/MACS2/

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written by jcs92 • jcs92

Do yourself a favor and use the virtual environment solution that Wouter suggested above. It is super-wasy to set up and simply typing source activate your-python2-environment is sufficient to activate it. That way you avoid messing around your two python versions that might do conflicting things plus additionally the use of both pip and conda which might cause trouble as well.

• 1 views • link
written by ATpoint ATpoint

In addition to Wouter's answer, you can use virtualenv to install MACS2:

# If virtualenv is not installed
#pip install virtualenv
virtualenv -p python2 ~/bin/MACS2
source ~/bin/MACS2/bin/activate
pip install numpy
pip install macs2
• 1 views • link
written by h.mon h.mon

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