palc / 2016

Materials prepared by the instructors of the #NGSchool2016

NGSchool2016 materials

Materials prepared by the instructors of the #NGSchool2016.

Table of content

• Introduction
• Server setup

Introduction

In order to initialise all dependencies, execute:

source /ngschool/.bashrc

Note, if you clone the repository in different directory than /ngschool, you will need to update NGSchoolDir in .bashrc file to this path ie. if you clone course materials in /home/lpryszcz/ngschool use:

NGSchoolDir=/home/lpryszcz/ngschool

How to obtain a copy

# copy all workshop materials (~15G)
rsync -avz [email protected]:/ngschool/ /ngschool --exclude='.git'

# alternatively use github (MUCH SLOWER!)
sudo apt-get install git-lfs
git lfs install
git clone [email protected]:NGSchool2016/ngschool2016-materials.git --recursive

Server setup

Requested software
If you have no github account or no read permission for given repository, use git clone https:// instead of git clone git@.

# admin
sudo apt install git htop screen wget python-pip python-dev cmake eog
sudo apt install libboost-all-dev libbz2-dev libtbb-dev
sudo apt install libboost-iostreams-dev libboost-system-dev libboost-filesystem-dev zlib1g-dev libgsl2

sudo -H pip install -U pip

# biotools
sudo apt install fastqc soapdenovo2 ray velvet mummer bwa samtools bedtools igv fastx-toolkit last-align python-biopython hmmer
sudo apt install python-numpy python-matplotlib
sudo -H pip install -U pysam

# tools for speakers
sudo apt install tophat bowtie bowtie2 idba ray tabix picard-tools igv 

# first update R to 3.3+ https://www.r-bloggers.com/how-to-install-r-on-linux-ubuntu-16-04-xenial-xerus/
sudo apt install blast2 tigr-glimmer exonerate muscle fasttree mcl r-base

mkdir src && cd src
# bin
git clone [email protected]:lpryszcz/bin.git

# FastQC
wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip
unzip fastqc_v0.11.5.zip && chmod +x FastQC/fastqc

# spades
wget http://spades.bioinf.spbau.ru/release3.9.0/SPAdes-3.9.0-Linux.tar.gz && tar xpfz SPAdes-3.9.0-Linux.tar.gz

# quast
git clone [email protected]:ablab/quast.git
(cd quast && ./setup.py install)

# redundans
git clone [email protected]:lpryszcz/redundans.git
## install SSPACE & GapCloser
wget -q http://www.baseclear.com/base/download/41SSPACE-STANDARD-3.0_linux-x86_64.tar.gz
tar xpfz 41SSPACE-STANDARD-3.0_linux-x86_64.tar.gz
ln -s SSPACE-STANDARD-3.0_linux-x86_64 SSPACE
wget -q -O- http://cpansearch.perl.org/src/GBARR/perl5.005_03/lib/getopts.pl > SSPACE/dotlib/getopts.pl
wget -q http://downloads.sourceforge.net/project/soapdenovo2/GapCloser/bin/r6/GapCloser-bin-v1.12-r6.tgz
tar xpfz GapCloser-bin-v1.12-r6.tgz
rm 41SSPACE-STANDARD-3.0_linux-x86_64.tar.gz GapCloser-bin-v1.12-r6.tgz GapCloser_Manual.pdf
## test
source /ngschool/.bashrc
(cd redundans && ./redundans.py -v -i test/*.fq.gz -f test/contigs.fa -o test/run1 --sspacebin $SSPACEBIN)

# trinity & transdecoder
git clone [email protected]:trinityrnaseq/trinityrnaseq.git
(cd trinityrnaseq && make)
git clone [email protected]:TransDecoder/TransDecoder.git
(cd TransDecoder && make)

# star
git clone --recursive https://github.com/alexdobin/STAR.git
(cd STAR && make STAR)

# salmon
git clone [email protected]:COMBINE-lab/salmon.git
(cd salmon && mkdir build && cd build && cmake -DBOOST_INCLUDEDIR=/usr/include/boost -DTBB_INSTALL_DIR=/usr/include/tbb .. && make)

# cufflinks
wget http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz
tar xpfz cufflinks-2.2.1.Linux_x86_64.tar.gz

# augustus
wget http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.0.2.tar.gz
tar xfpz augustus-3.0.2.tar.gz 
(cd augustus-3.0.2/src && make)

# GATK & snpEff

wget http://downloads.sourceforge.net/project/snpeff/snpEff_latest_core.zip && unzip snpEff_latest_core.zip

# Bismarc
git clone [email protected]:FelixKrueger/Bismark.git
wget http://smithlabresearch.org/downloads/preseq_linux_v2.0.tar.bz2 && tar -jxvf preseq_linux_v2.0.tar.bz2
wget https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.2.zip && unzip qualimap_v2.2.zip
wget http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/trim_galore_v0.4.1.zip && unzip trim_galore_v0.4.1.zip

# 
sudo -H pip install git+https://github.com/ewels/MultiQC.git

git clone [email protected]:parseq/convector.git

# GATK https://software.broadinstitute.org/gatk/download/auth?package=GATK
(mkdir GATK && cd GATK && tar jxvf ../GenomeAnalysisTK-3.6.tar.bz2)

# InterProScan https://www.ebi.ac.uk/interpro/interproscan.html

# clean-up
rm *.zip *.gz *.bz2

# jmarzec
# sudo R
source("http://bioconductor.org/biocLite.R"); biocLite("affy")
source("http://bioconductor.org/biocLite.R"); biocLite("affyPLM")
source("http://bioconductor.org/biocLite.R"); biocLite("arrayQualityMetrics")
source("http://bioconductor.org/biocLite.R"); biocLite("biomaRt")
source("http://bioconductor.org/biocLite.R"); biocLite("gcrma")
source("http://bioconductor.org/biocLite.R"); biocLite("geneplotter")
install.packages("gplots")
source("http://bioconductor.org/biocLite.R"); biocLite("hgu133acdf")
source("http://bioconductor.org/biocLite.R"); biocLite("hgu133plus2.db")
source("http://bioconductor.org/biocLite.R"); biocLite("limma")
source("http://bioconductor.org/biocLite.R"); biocLite("simpleaffy")
source("http://bioconductor.org/biocLite.R"); biocLite("sva")

# lpryszcz
source("http://bioconductor.org/biocLite.R"); biocLite("DESeq")
source("http://bioconductor.org/biocLite.R"); biocLite("DESeq2")
source("http://bioconductor.org/biocLite.R"); biocLite("cummeRbund")

# rhamilton
install.packages("devtools")
library(devtools)
install_github("al2na/methylKit", build_vignettes=FALSE, 
  repos=BiocInstaller::biocinstallRepos(),
  dependencies=TRUE)

# mlapinski
install.packages('caTools')
source('http://bioconductor.org/biocLite.R'); biocLite('Rsamtools')
library(devtools); install_github("hms-dbmi/spp")

If you get an error Package 'igv' has no installation candidate, make sure the "multiverse" repository is enabled. Try this:

echo 'deb http://archive.ubuntu.com/ubuntu/ xenial multiverse' >> /etc/apt/sources.list

In the case IGV hangs, you can try running it from the website. Navigate to: http://www.broadinstitute.org/software/igv/download, select appropriate version (2GB is the safest) and press Launch.