Chapter Ensemble

In this chapter, I will discuss all setups for the work environment before starting analysis.

This page contains quick steps for creating same work environment in 5 mins.

The following pages will explain details:

1. All About Installations: How to install python, python packages, and other bioinformatic programs related to this book.

2. Keep Running: How to keep your command running in the shell.

3. Coding Environment: Using Jupyter Notebook/Lab for data analysis, and useful tips to enhance efficiency.

4. Git and Github: Using Git and Github while you do coding and analysis.

5. Other tips: Some other optional tips.

Step 1. Installation

1.1 Install minicoda or anaconda

Install any one of them from here: miniconda or anaconda

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

These are my selections

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.

file in py_genome_sci_book/analysis/hello_world/jupyter_hello_world.ipynb

Now everything is installed!