Smithsonian/vagrant-stacks

Name: vagrant-stacks

Owner: Smithsonian Institution

Description: Vagrant launcher for STACKS

Created: 2013-09-30 16:54:41.0

Updated: 2015-02-27 14:38:10.0

Pushed: 2015-08-06 17:12:12.0

Homepage: null

Size: 124

Language: Shell

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README

vagrant-stacks

Vagrant launcher for STACKS 1.34 (http://creskolab.uoregon.edu/stacks)

This creates a VM on your computer running STACKS that can be used to run the command line tools and web interface of STACKS.

Requirements

• Download and install VirtualBox (https://www.virtualbox.org/)
• Download and install Vagrant (http://www.vagrantup.com/)
• Download and install git if not installed (http://git-scm.com/download)

Installation

 clone https://github.com/Smithsonian/vagrant-stacks.git
vagrant-stacks
rant up

Use

• To access the stacks web interface Point your browser at http://localhost:8082/stacks. You should see the Stacks webpage

• To use the stacks command line tools Login to the VM command line vagrant ssh

• To setup a database use:

  l -u dbuser -pdbpass -e "CREATE DATABASE redseaexp_radtags"
  l -u dbuser -pdbpass redseaexp_radtags < /usr/share/stacks/sql/stacks.sql
  

Getting to files for analysis

• By default only files in the conf folder in the vagrant-stacks folder will be accessible in the VM in the /vagrant directory
• To get to other files, In Vagrantfile uncomment the line: #config.vm.synced_folder "/Users/", "/hostfiles" The example will take the folder /Users on the host computer and make it available as /hostfiles on the VM
• From the host use vagrant reload to use the new settings

VM Configuration (optional)

• Specify the number of CPUs to use with “v.cpus = 1”
• Specify the RAM the VM should use with “v.memory = 2048”
• From the host use vagrant reload to use the new settings

Stacks configuration used

• Default mysql username= dbuser password= dbpass
• Command line tools are installed in /usr/local/bin
• Web resources are in /usr/share/stacks

Vagrant basics

To access the command line of the vagrant VM type: vagrant ssh

To suspend the VM (save the current state) use: vagrant suspend

To reboot the VM with new configuration from the file Vagrantfile (e.g. RAM, CPUs) : vagrant reload

To destroy the VM (lose all data not stored in /vagrant or /hostfiles if you configured that) use: vagrant destroy