README for BiocNimfa

One strategy

• DESCRIPTION:PythonRequirements: lists python version and packages.

• BiocNimfa/python-requirements.txt contains output of pip freeze

• build system creates a ~/.virtualenvs/<BiocPkgName> virtual environment (could be anywhere) with python and packages

    virtualenv -p python3.5 ~/.virtualenvs/<BiocPkgName>
  

• activate virtualenv

  source ~/.virtualenvs//bin/activate

• install python requirements

  pip install -r python-requirements.txt

• deactviate virtualenv

  deactivate

• build system sets

    export RETICULATE_PYTHON=~/.virtualenvs/<BiocPkgName>/bin/python
  

• R -e "reticulate::import('nimfa')" works!

Second strategy

Installation Commands

virtualenv ~/.virtualenvs/BiocNimfa
source ~/.virtualenvs/BiocNimfa/bin/activate
pip install -r BiocNimfa/python_requirements.txt
deactivate

Shell + R commands

shell:

Activate virtualenv before using reticulate or starting R.

source ~/.virtualenv/BiocNimfa/bin/activate

R:

Load BiocNimfa and import the module with function nimfa()

library(BiocNimfa)
nimfa = nimfa()

R:

Run test cases included in BiocNimfa

devtools::test()