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caseywdunn / postdoc_dunnlab_2018.md
Last active May 21, 2018
Postdoc position: HIV phylogenetics in the Dunn Lab at Yale University
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View conda.md

Working with Conda

First, some nomenclature (see https://conda.io/docs/glossary.html for more):

  • A recipe is a flat directory that has the information needed to build a package
  • A package is a "compressed file that contains everything that a software program needs in order to be installed and run... You manage conda packages with conda."
  • An environment is a "directory that contains a specific collection of conda packages and their dependencies, so they can be maintained and run separately without interference from each other."

A typical workflow:

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caseywdunn / PCfB_Regular_Expressions.md
Last active Sep 25, 2017
Regular expressions intro and examples
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caseywdunn / evol2017.md
Last active Mar 5, 2018
Notes to accompany my talk.
View evol2017.md

Evolution 2017

June 25, 2017 (and updated since then)

Casey Dunn, http://dunnlab.org , @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.

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caseywdunn / docker.md
Last active Sep 28, 2021
Docker cheat sheet
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Docker cheat sheet

Introduction

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
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caseywdunn / genomics2016.md
Last active Oct 30, 2016
Notes from my October 7, 2016 talk at the Boston Evolutionary Genomics Supergroup Meeting
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caseywdunn / macos_virtualenv.sh
Created Jun 24, 2016
Setup and examples of virtualenv on osx
View macos_virtualenv.sh
# 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
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caseywdunn / TREE_tree.tre
Created May 14, 2015
Newick representation of the phylogenetic tree in Figure 1 of our TREE review on animal phylogenetics (http://dx.doi.org/10.1146/annurev-ecolsys-120213-091627)
View TREE_tree.tre
(
Ctenophora,
(
Porifera,
(
Placozoa,
(
Cnidaria,
(
Xenacoelomorpha,