Problems installing ete3 using conda

Question

[jyu429]

Hi,

I'm having some trouble installing ete3 using the recommended conda way. I first ran conda install -y pip six numpy pyqt lxml gcc to install all the dependencies, but then when I ran conda install -c etetoolkit ete3 ete3_external_apps I was met with this error:

UnsatisfiableError: The following specifications were found to be in conflict:
  - ete3_external_apps -> python 2.7* -> openssl 1.0.1*
  - python 3.6*
Use "conda info <package>" to see the dependencies for each package.

Is this implying that my python 2.7 is conflicting with the current python 3 version?

[shunyip]

I had a similar error from installing a different package. I solved it by removing everything that are in conflict (including python itself), and then installing what I need (in your case, ete3). This way, conda should also install python again because it's one of the dependencies.

I hope this helps,

[Joe]

Are you trying to do this inside a virtualenv?

[jyu429]

No, I don't think so.

[Joe]

You could try it as such? Using virtualenvs often solved package conflicts etc.

Answer 1

[Madhuran Thiagarajah]

I had a similar problem when trying to install some other packages. I found this thread where one user suggested running:

conda install python=3.5

my problem was resolved after:

conda install python=2.7

then running the command for my package installation.

Answer 2

[heronoh]

thanks Madhuran Thiagarajah!
the full solution that worked for me is:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh                                                                                                                      
 chmod a+x Miniconda3-latest-MacOSX-x86_64.sh
conda config --set auto_activate_base false
conda install python=2.7
conda install -c etetoolkit ete3 ete_toolchain

[ATpoint]

I strongly recommend to make a separate environment before installing python2 into your python3-driven base environment.