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caseywdunn / ubuntu_amazon_tarball.sh
Last active Aug 29, 2015
Agalma installation scripts
View ubuntu_amazon_tarball.sh
# 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
@caseywdunn
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,
@caseywdunn
caseywdunn / genomics2016.md
Last active Oct 30, 2016
Notes from my October 7, 2016 talk at the Boston Evolutionary Genomics Supergroup Meeting
View genomics2016.md
@caseywdunn
caseywdunn / PCfB_Regular_Expressions.md
Last active Sep 25, 2017
Regular expressions intro and examples
View PCfB_Regular_Expressions.md
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:

@caseywdunn
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.

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