03_Conda
By Yan Li
PhD in Bioinformatics, University of Liverpool
How do we install softwares in Linux?
- Compile from source code
- Download the binary file
- Use a package manager
from the system:
apt-get
(Debian, Ubuntu),yum
(CentOS, Red Hat),pacman
(Arch, Manjaro),homebrew
(Macos)from a programming language:
pip
(Python),cran
(R)Universal package manager:
conda
- Use a container:
docker
,singularity
Virtual environment
# conda environments:
#
base /home/yan/anaconda3
ai /home/yan/anaconda3/envs/ai
bioinfo /home/yan/anaconda3/envs/bioinfo
course * /home/yan/anaconda3/envs/course
Put conflicting packages in seperate environments
Manage packages
# packages in environment at /home/yan/anaconda3/envs/course:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main conda-forge
blast 2.9.0 h20b68b9_1 bioconda
boost 1.68.0 py37h8619c78_1001 conda-forge
boost-cpp 1.68.0 h11c811c_1000 conda-forge
...
Manage dependencies automatically
Basic commands
# environment
conda create -n env-name
conda env list
conda activate env-name
conda deactivate
# package
conda install package-name
conda remove package-name
conda list