Friday, November 27, 2020

Conda - A must-have for bioinformatician

As a bioinformatician, when you are given a new system (Mac, HPC, or any Linux environment), the first thing to do is probably to configure your work environment, install required tools, etc. 

Here is what I did for the new Mac:

1. This step is optional. Apple changed to default shell to zsh since the last OS. If you like bash, you can change the default zsh shell from bash:

chsh -s /bin/bash

2. Install Miniconda. Miniconda is a free minimal installer for conda, incl. only the basic ones (e.g. conda, python, zlib, etc). If you are under Linux, download the one for Linux

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh

bash Miniconda3-latest-MacOSX-x86_64.sh

3. Install commonly used tools with bioconda:

# update bash (the one coming with MacOS is too old)

conda install -c conda-forge bash

# samtools etc.

conda install -c bioconda samtools plink plink2

# UCSC Kent Utilities etc.

conda install -c bioconda ucsc-bedgraphtobigwig ucsc-wigtobigwig ucsc-liftover ucsc-bigwigsummary

# GNU coreutils etc.

conda install -c bioconda coreutils gawk wget

# R and R package etc.

conda install -c r r-base

conda install -c r r-essentials

conda install -c r r-tidyverse

# Google cloud gsutil

conda install -c conda-forge gsutil 

Life is much easier after conda!

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