Installing a PhyloStack - cdoorenweerd/PhylOStack GitHub Wiki

This HOWTO explains how to install a PhylOStack in OpenStack with Ubuntu 14.04 LTS.

Creating an instance with the PhylOStack

  1. Launch a new instance from the OpenStack dashboard
  2. Select the Ubuntu 14.04 image
  3. Select a suitable flavour, at least 8 VCPU and 8 RAM is recommended
  4. Insert the following script in the customization tab:
#!/bin/sh
#
sudo apt-get -y update
sudo apt-get -y install git htop
cd /usr/local
sudo git clone https://github.com/cdoorenweerd/PhylOStack.git

The actual software packages are installed from a collection of installation scripts, where you may choose to install some, or all. Simply SSH into the instance and use the following commands. You can also install these at a later time. Everything combined, including OS, will take about 5.5GB of disk space.

To install all software with one command use:

bash /usr/local/PhylOStack/install_all.sh

The machine will reboot after installing all the software. The installation will take about 15 minutes. Alternative to installing all the software at once, use the package specific installation scripts to install your own selection:

bash /usr/local/PhylOStack/bamm.sh
bash /usr/local/PhylOStack/beast_beagle_phyml.sh
bash /usr/local/PhylOStack/exabayes.sh
bash /usr/local/PhylOStack/mafft.sh
bash /usr/local/PhylOStack/miniconda_ete3_partitionfinder.sh
bash /usr/local/PhylOStack/p4.sh
bash /usr/local/PhylOStack/raxml_rnr.sh
bash /usr/local/PhylOStack/r_dendextend_bammtools.sh
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