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caseywdunn /
Last active August 10, 2023 18:13
Docker cheat sheet

Docker cheat sheet


Docker is a tool for bundling together applications and their dependencies into images that can than be run as containers on many different types of computers.

Docker and other containerization tools are useful to scientists because:

  • It greatly simplifies distribution and installation of complex work flows that

Using samtools

This is my own exploration of samtools behavior and snippets of code I use in my own analyses.

The data

I am using the GRCh38 human reference from December, 2013.

There are two focal datasets of reads:

# The catalytic converter theft chain
Just had the second attempted theft of our catalytic converter. Here is a bit about context.
## Theft and fencing
I am not sure at what point the contraband enters the legitimate supply chain.
caseywdunn /
Created June 24, 2016 18:17
Setup and examples of virtualenv on osx
# Setting up virtualenv on macOS Yosemite
brew update
brew upgrade
which python # check location of system version
brew install python
brew install freetype # Needed by some python packages
brew install libxml2 # Needed by some python packages
pip install virtualenv virtualenvwrapper pytest
caseywdunn /
Last active May 21, 2018 17:27
Postdoc position: HIV phylogenetics in the Dunn Lab at Yale University
caseywdunn /
Last active March 5, 2018 22:36
Notes to accompany my talk.

Evolution 2017

June 25, 2017 (and updated since then)

Casey Dunn, , @caseywdunn

These are some notes and annotated references relevant to my talk with Stacey Smith in the symposium "SSB Symposium Phylogenetic approaches to connecting genotypes to phenotypes" at Evolution 2017.

If you are interested in any of this work let me know. I am moving to Yale and looking for people to join the new research group.