Bioinfo rio vagrant

A vagrant version of the rio vagrant analysis machine

The published vagrant box can be found at https://app.vagrantup.com/abhi18av/boxes/ITGE2017_RIO

For desktop setup, refer https://linuxhint.com/mount_vmware_shares_command_line_linux_vm/

Setup Instruction

Digital Ocean

• Things work fine by default

Scaleway

• Provider : Scaleway
• OS : Ubuntu Xenial 16.04
• Architecture : x86_64

Steps on Scaleway

• Build Kernel
• Setup virtualbox

Step 3

• Setup nix pkg manager

Step 4

• Install vagrant

Step 5

• Setup the ITGE2017 vagrant box

TODO - install ncbi blast for v2.0.0

https://github.com/enormandeau/ncbi_blast_tutorial

Download link

ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.9.0+-x64-linux.tar.gz

setup commands

• From Host

cd /biodragon/vagrantBox/

rclone copy onedrive-em:ncbi_blast_2.9.0_x64_linux.tar.gz ./

tar -xvzf ncbi_blast_2.9.0_x64_linux.tar.gz 

• From Guest

cd /vagrant/
sudo cp -a ncbi-blast-2.9.0+ /opt/
cp -a ncbi-blast-2.9.0+ /opt/

# add this to the .bashrc
export PATH="/opt/ncbi-blast-2.9.0+/bin/":$PATH

SPOTYPING SETUP

https://github.com/xiaeryu/SpoTyping-v2.0

RD ANALYZER SETUP

https://github.com/xiaeryu/RD-Analyzer

KVARQ SETUP

• Inside the guest machine

sudo yum install python-devel 
wget https://github.com/kvarq/kvarq/archive/master.zip
unzip master.zip
rm master.zip
cd kvarq-master
python setup.py test
sudo python setup.py install

Change the default init directory to /vagrant/ for the vagrant ssh in host.

building a box from scratch

https://medium.com/@gajbhiyedeepanshu/building-custom-vagrant-box-e6a846b6baca

https://www.engineyard.com/blog/building-a-vagrant-box-from-start-to-finish

https://scotch.io/tutorials/how-to-create-a-vagrant-base-box-from-an-existing-one

• Command to remove all the vagrant boxes

vagrant box list | cut -f 1 -d ' ' | xargs -L 1 vagrant box remove -f

• Add an existing box

vagrant box add my-box name-of-the-box.box
vagrant init my-box
vagrant up