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NGSchool2018 materials

Materials prepared by the instructors of the #NGSchool2018.

You can sync all data using (don't do it during workshops!):

rsync -avz --exclude="*.git/" USERNAME@192.168.1.111:/ngschool/2018 ~/ngschool
# and type your password

Table of Contents

Dependencies

In order to run workshop examples in your own laptop, you'll need to install all below prerequesities.
Note, the installation instructions are meant for Ubuntu 18.04. Everything should be done in below order, it may take a few hours (especially compilation of R packages is lengthy...) and around 15-20GB of hard-drive space.

bioconda & docker

# install conda ie. in /ngschool/src/miniconda2
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh 

# configure bioconda channels
#(conda config --add channels r)
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

# install dependencies - AVOID INSTALLING r-base, as it'll mess up with native R installation
conda install nanonet nanocall poretools spades miniasm racon blasr minimap2 ngmlr bwa edlib mummer nanopolish
conda install delly manta snpeff vcfanno seqtk samtools igv survivor bandage quast busco bedtools
conda install canu tablet

Ubuntu

sudo apt install htop git python-pip python3-pip libxml2-dev libcurl4-openssl-dev libssl-dev last-align poretools deepnano

PIP & PIP3

sudo pip install -U biopython matplotlib seaborn pandas cython numpy h5py Theano python-dateutil

# albacore ie. read_fast5_basecaller.py + all dependencies
sudo pip3 install 2018/src/whl/ont_albacore-2.3.3-cp36-cp36m-manylinux1_x86_64.whl
## note above is for Python 3.6 (default in Ubuntu 18.04),
## for Python 3.4 or 3.5 just find respective .whl file in the same directory

R, Bioconductor and other R packages

# R - need to add R repo first
echo "deb https://www.stats.bris.ac.uk/R/bin/linux/ubuntu $(lsb_release -c | xargs | cut -f2 -d' ')/" | sudo tee -a /etc/apt/sources.list
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
sudo apt-get update && sudo apt upgrade && sudo apt install libcurl4-openssl-dev libxml2-dev libcairo2-dev libxt-dev libssl-dev
sudo apt install r-base r-base-dev

# install R packages for all users
sudo R | tee -a /tmp/r.log

# CRAN packages
install.packages('tidyverse')
install.packages('data.table')

# devtools ie to install from github
install.packages('devtools')
devtools::install_github('gabraham/flashpca/flashpcaR')

# bioconductor
source("https://bioconductor.org/biocLite.R") 
biocLite('BiocInstaller');
biocLite('GenomicRanges');

MinKNOW

sudo apt-get install wget
wget -O- https://mirror.oxfordnanoportal.com/apt/ont-repo.pub | sudo apt-key add -
echo "deb http://mirror.oxfordnanoportal.com/apt xenial-stable non-free" | sudo tee /etc/apt/sources.list.d/nanoporetech.sources.list

sudo apt-get update
sudo apt-get install minknow-nc

Running exercises

Working in your own laptop

Copy workshop materials locally ie. rsync -avz --exclude="*.git/" USERNAME@192.168.1.111:/ngschool/2018 ~/ngschool, enter NGSchoool directory cd ~/ngschool/2018 and you are ready to work. Make sure, you have installed all prerequesities before!

Working in remote NGSchool server

Login to the server with your credentials, sync workshop materials to your home directory rsync -av --exclude '*.git/' /ngschool/2017 ~/ngschool, enter your personal NGSchoool directory cd ~/ngschool/2017 and you are ready to work.

Make sure to import local variable in each new window

# NOTE: you may need to change `/ngschool/2018` directory
# if you cloned the repository to another location
source /ngschool/2018/.bashrc

Working in VirtualBox

!!!TBD!!! First, get VM image and create VM in VirtualBox using this image. Then run VM (u: ngschool p: ngschool), enter NGSchoool directory cd /ngschool/2017 and you are ready to work.

Cloning the repository

This has to be done only if you wish to explore materials before the school. Otherwise, ignore below.
Cloning and syncing from github [before or after the school]

# get fresh copy of the repo
mkdir -p ~/ngschool && cd ~/ngschool
git clone --recursive https://github.com/NGSchoolEU/2018.git

# or sync repo to the latest version
cd ~/ngschool/2018
git pull

Below, we're providing links to data not included in this repository.

Materials not included in github repo

You can get below using wget -nc -r -np HTTP

Note, you can also sync all data using:

rsync -avz --exclude="*.git/" USERNAME@192.168.1.111:/ngschool/2018 ~/ngschool
# and type your password