cmap / cmapPy

Assorted tools for interacting with .gct, .gctx files and other Connectivity Map (Broad Institute) data/tools
https://clue.io/cmapPy/index.html
BSD 3-Clause "New" or "Revised" License
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how I create a conda environment for cmapPy and python 3 #57

Open ghost opened 5 years ago

ghost commented 5 years ago

Not sure if this useful for others / including in docs, but here's how I create a conda environment for cmapPy in python 3. I mention this b/c I have done it other ways and ended up not having the hdf5 command line tools in the environment (which I find useful).

  1. conda create -n cmapPy3 python=3 scikit-learn scipy numpy seaborn matplotlib statsmodels pandas jupyter sympy h5py
  2. conda activate cmapPy3
  3. pip install cmappy
  4. try it out!
    1. should have hdf5 command line tools

(NB: not installing h5py via conda, and instead having pip install it as a dependency of cmappy caused me to not have the command line tools for whatever reason). Obvs this also includes some other analysis libraries / tools I find useful.

levlitichev commented 5 years ago

^^ this worked for me too