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I'm using snakemake with conda env.

I created conda environment like conda create -n myenv some_packages after that I used pypy3 to install other packages, like.
pypy3 -m some_package pypy3 -m pip install --no-cache-dir some_package

Now I exported the env in this way conda env export > myenv.yaml

But when the yaml file used by snakemake it does not install the packages that were installed using pypy3.

Any suggestions?

Thanks

Medhat
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    preferably you don't mix different environment managars. Can you install the package with conda as well? – Maarten-vd-Sande Jan 30 '20 at 20:23
  • Do you mean instead of `pypy3 -m some_package` I should use `conda install some_package`. It is a good suggestion, but the conda environment has the Pypy3 intepreter installed, but one Pypy3 package `intervaltree` is still missing. The reason why this is not installed by default is that this is not yet available in any conda repositories. as a result I used `pypy3 -m pip install --no-cache-dir intervaltree==3.0.2` – Medhat Jan 30 '20 at 23:08
  • I actually never heard of pypy3 before, and I thought it was something like pip! I am not sure how to do this. You could always try to add it to for instance conda-forge and then it will be conda installable. – Maarten-vd-Sande Jan 31 '20 at 08:04
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    Would it be okay for you to manually add the entries in the myenv.yaml? – Maarten-vd-Sande Jan 31 '20 at 08:38
  • I will try that, and see if it will work. – Medhat Jan 31 '20 at 22:04

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