Linux Software Installation - Cornell University

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 ("#!")

Read BioHPC software instruction pages: R: Rstudio:

Python: Jupyter:

Conda:

Write permissions when installing software

/usr

/usr/local

/home/xxxxx /workdir

Root user has write privilege.

You have write privilege.

* When installing software, some modification might be needed to install in $HOME

Python

PYTHON

PERL

Repository

PYPI *

CPAN

Installation tool pip

cpan

Library PATH PYTHONPATH PERL5LIB

* pronounced "pie pee eye"

R CRAN install.packages

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