0Record-setup

# To create a working python environment for gainsaw, something like the
# following will work.

# 1. Set up conda to manage our python environment:
#
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash ./Miniconda3-latest-Linux-x86_64.sh 

# 1.1. Open a new shell and type:
#
conda config --set auto_activate_base false

# 1.2. Open a new shell and type:
#
conda env list
\rm Miniconda3-latest-Linux-x86_64.sh


# 2. Now create an environment for gainsaw development:
#
conda create --name gainsaw
conda activate gainsaw
conda install python=3.11.3 anaconda
conda install Cython
pip install build
pip install biopython


# 3. Install pybedtools (required for gainsaw) and pyliftover (our
#    original template for gainsaw) into the gainsaw environment:
#
git clone https://github.com/daler/pybedtools.git
cd pybedtools/
### Temporary fix to pybedtools as per github notes:
###
sed -i -e "1a # cython: language_level=2"  pybedtools/cbedtools.pyx
sed -i -e "1a # cython: language_level=2"  pybedtools/featurefuncs.pyx
sed -i -e "1a # cython: language_level=2"  pybedtools/_Window.pyx
sed -i -e "287a \        language_level=2,"  setup.py
###
python setup.py build
python setup.py install
cd ..

git clone https://github.com/konstantint/pyliftover.git
conda deactivate gainsaw


# 4. From now one, work on gainsaw in the gainsaw environment; e.g., to
#    build the latest version:
#
git clone https://github.com/vpbrendel/GAinSAW.git
cd GAinSAW

# ... first-time setup; or "cd GAinSAW; git pull origin main" for updating.
#
conda activate gainsaw
cd gainsaw
python -m build
python -m pip install .
cd ..