genomics-VM

Setup your development environment for genomics applications easily by setting up a Virtualbox VM through Vagrant.

Prerequisite

• Vagrant > 2.0
• Virtual Box

Installation

• Install vagrant-vbguest vagrant plugin:

  vagrant plugin install vagrant-vbguest

• Build the vagrant box

    git clone https://github.com/NAL-i5K/genomics-VM
    cd genomics-VM
    vagrant up

• You are done ! Wait for VM restart and you can login CentOS through vagrant user with password vagrant.

What kind of environment is settled up in VM ?

General purpose

• CentOS 6.9
• git 2.24
• Python 2.7.15
• samtools 1.9
• wigToBigWig
• wiggle-tools
• bam_to_bigwig
• coordinate_conversion
• genomics-workspace (including python virtual environment with name py2.7)
• jbrowse

i5K-only tools

• apollo2_data_build_script