caseywdunn

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

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

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.

caseywdunn

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

caseywdunn

# 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