Linux Software Installation
Linux Software Installation
Part 2
Qi Sun Bioinformatics Facility
Two conda distributions
Miniconda: minimum distribution
Anaconda: full distribution
Conda channels (repositories)
$HOME/.condarc
bioconda anaconda conda-forge
conda install -c bioconda
From
Shared libraries
to
Dedicated libraries for each application
Docker containers
Container1 Container2 Container3
Ubuntu Debian CentOs Linux Linux Linux
Host OS Kernel Hardware infrastructure ? File system and network port are contained;
Conda environments
Env.1 Env.2 Env.2
app1 app2
app3
Host OS
Hardware infrastructure
? Modified $PATH; ? File system not isolated;
Binary
Human readable source
Compile
(optimized)
Binary software
? Hardware & OS dependent
Script
Human readable script
Run
Through
? Independent of
Interpreter hardware & OS
Byte Human
Compile
Run
Byte
Through RTE
code readable source
code
(run time environm?ent)Independent of
hardware & OS
Two modes to run interpreter:
SHELL
$ python >>>import os >>>os.listdir()
Batch script *
$ python myscript.py
* Alternatively, using shebang line ("#!")
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