1.2 Setup python environment and packages for this book
# setup conda channels
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
# remove the incomplete environment if you did
conda env remove -n genome_book
# create the environment and install everything in one command!
# These packages will be used in this book
conda create -n genome_book \
python=3.7 \
pandas==1.0.3 \
seaborn=0.10.0 \
jupyter==1.0.0 \
jupyter_contrib_nbextensions==0.5.1 \
scikit-learn==0.22.2.post1 \
pysam==0.15.4 \
deeptools==3.4.2 \
pybedtools==0.8.1 \
scanpy=1.4 \
salmon==1.2.1
1.3 Use screen to start jupyter notebook
# this creates a new screen named jupyter
screen -R jupyter
# In the new screen
# go back to your home direcotry
cd ~
# jupyter can only read file from the directory it starts,
# if you run the jupyter in a subdirectory,
# it can not reach other files on your computer.
# enter the env
conda activate genome_book
# optionally, setup your jupyter password
jupyter notebook password
# start jupyter notebook
jupyter notebook
# jupyter will keep running in the screen even if you cloase the terminal
# You should see the jupyter URL from its stdout
1.4 In jupyter notebook extension tab, select your favorite extensions
1.5 clone the repository from github
$ cd /To/The/Place/You/Want/To/Save/This/Repo/
$ git clone https://github.com/lhqing/py_genome_sci_book.git
Now in jupyter notebook navigator, go to the github repo, you can start browse my code and data.
