Setup for https://github.com/PacificBiosciences/kineticsTools, two ways

readme.md

You can create the environment manually like so:

python3 -m venv venv
source venv/bin/activate
pip install git+http://github.com/PacificBiosciences/pbcore \
    git+https://github.com/PacificBiosciences/pbcommand \
    git+https://github.com/PacificBiosciences/kineticsTools

You can then run pip list to see the versions installed:

(venv) ~ pip list
Package       Version
------------- ----------
avro-python3  1.9.2.1
biopython     1.77
certifi       2020.4.5.2
chardet       3.0.4
idna          2.9
iso8601       0.1.12
kineticsTools 0.7.0
numpy         1.18.5
pbcommand     2.1.1
pbcore        2.1.4
pip           19.2.3
pyBigWig      0.3.17
pysam         0.16.0
pytz          2020.1
requests      2.23.0
scipy         1.4.1
setuptools    41.2.0
urllib3       1.25.9

For this your python3 will need to be >=3.7

---

Using conda to create an environment:

conda env create -f kineticsTools.yaml
conda activate kinetics_tools

kineticsTools.yaml

name: kinetics_tools
channels: 
  - bioconda
  - conda-forge
  - defaults
dependencies:
  - python>=3.7
  - pip
  - pip:
    - git+http://github.com/PacificBiosciences/pbcore 
    - git+https://github.com/PacificBiosciences/pbcommand 
    - git+https://github.com/PacificBiosciences/kineticsTools