Other Tips

Oh my zsh

Bash is the most common shell, but there are a lot more other options. My favorite shell is zsh, when equip with "Oh my zsh".

GitHub - ohmyzsh/ohmyzsh: 🙃 A delightful community-driven (with 2,000+ contributors) framework for managing your zsh configuration. Includes 300+ optional plugins (rails, git, macOS, hub, docker, homebrew, node, php, python, etc), 140+ themes to spice up your morning, and an auto-update tool so that makes it easy to keep up with the latest updates from the community.GitHub

Give it a try, and you will love it.

Customize your shell using the config file

Both bash and zsh comes with a config file in your home directory. The one for bash is ~/.bashrc and the one for zsh is ~/.zshrc.

This config file is basically a shell script, execute by the shell when it starts. Usually, I create many alias for common commands such as ssh to a server or start a jupyter notebook, zsh also come with many convenient alias and other fancy plugins and themes for your shell (I use ys theme).

Export your environment for backup and recovering

From this stack overflow and export section of conda documentation:

# enter env first
$ conda activate genome_book
(genome_book)

# export the environment into a yml file, which contains all installation history
$ conda env export --from-history > environment.yml
(genome_book)

# This is the content of that file
$ cat environment.yml
name: genome_book
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - pandas==1.0.3
  - jupyter==1.0.0
  - scikit-learn==0.22.2.post1
  - pysam==0.15.4
  - seaborn=0.10.0
  - pybedtools==0.8.1
  - python=3.7
  - jupyter_contrib_nbextensions==0.5.1
  - deeptools==3.4.2
prefix: /Users/hq/miniconda3/envs/genome_book
(genome_book)

# recreate the exact environment with the yml file
$ conda env create -f environment.yml