Casey Dunn caseywdunn

Boston Evolutionary Genomics Supergroup Meeting

October 7, 2016

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

These are some notes and annotated references from my talk at the Boston Evolutionary Genomics Supergroup Meeting.

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

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.

These examples of regular expressions are taken largely from our book Practical computing for Biologists. More information is available at http://practicalcomputing.org.

This document can be accessed via the delightful github url shortener at https://git.io/dine

Given the following names:

Agalma elegans

Frillagalma vitiazi

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:

Postdoc position: HIV phylogenetics at Yale University

Please share this link to the ad: https://git.io/yale_postdoc_2018

Advisor: Casey Dunn

Location: Department of Ecology and Evolutionary Biology, Yale University, in New Haven, Connecticut, USA

Application due date: June 1, 2018 (or until filled)

Harvard Systems Biology Theory Lunch

Short url: https://git.io/fjchB

10 May 2019

Casey Dunn

Animal diversity and the Hubble deep field

	# This is a full set of commands to install [Agalma](https://bitbucket.org/caseywdunn/agalma)
	# from the on Ubuntu Server from the tarballs. It has been tested on the AWS Ubuntu Server AMI.
	#

	sudo apt-get update
	sudo apt-get install make

	wget https://bitbucket.org/caseywdunn/biolite/raw/master/install_biolite_ubuntu.sh
	sudo sh install_biolite_ubuntu.sh
	wget https://bitbucket.org/caseywdunn/agalma/raw/master/install_agalma_ubuntu.sh

	(
	Ctenophora,
	(
	Porifera,
	(
	Placozoa,
	(
	Cnidaria,
	(
	Xenacoelomorpha,

	# 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