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2019_AWS_Setup.md

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Notes and procedure on creating instance

Need to work in N. Virginia

AWS_Setup

Base Instance Creation

Contents of Base Instance

  1. Free-tier Ubuntu 18.04 LTS AMI
  2. 2 Core, 4 Gb RAM
  3. 30Gb EBS storage
  4. Security, All TCP
  5. Elastic IP (Since been released)

Updating and installing VNC and Desktop

sudo apt-get update
sudo apt-get upgrade
sudo vim /etc/ssh/sshd_config
##Change PasswordAuthentication to yes from no, then save and exit.
sudo /etc/init.d/ssh restart
sudo passwd ubuntu #"Genomics"
sudo apt install xfce4 xfce4-goodies
cd /usr/local/src
sudo wget https://bintray.com/tigervnc/stable/download_file?file_path=tigervnc-1.9.0.x86_64.tar.gz
sudo tar -xzvf download_file\?file_path\=tigervnc-1.9.0.x86_64.tar.gz
sudo rm download_file\?file_path\=tigervnc-1.9.0.x86_64.tar.gz
cd /usr/local/bin
cp -s ../src/tigervnc-1.9.0.x86_64/usr/bin/* .
cd
vncserver #"Genomics"
vncserver -kill :1
mv ~/.vnc/xstartup ~/.vnc/xstartup.bak
nano ~/.vnc/xstartup

Pasted the following into ~/.vnc/xstartup

#!/bin/bash
xrdb $HOME/.Xresources
startxfce4 &

Exited ~/.vnc/xstartup and now in terminal

sudo chmod +x ~/.vnc/xstartup
vncserver
sudo nano ~/.config/xfce4/xfconf/xfce-perchannel-xml/xfce4-keyboard-shortcuts.xml

change

<property name="&lt;Super&gt;Tab" type="string" value="switch_window_key"/>

to

<property name="&lt;Super&gt;Tab" type="empty"/>

Exit to terminal

sudo nano /etc/systemd/system/[email protected]

Add

[Unit]
Description=Start TigerVNC server at startup
After=syslog.target network.target

[Service]
Type=forking
User=ubuntu
Group=ubuntu
WorkingDirectory=/home/ubuntu

PIDFile=/home/ubuntu/.vnc/%H:%i.pid
ExecStartPre=-/usr/local/bin/vncserver -kill :%i > /dev/null 2>&1
ExecStart=/usr/local/bin/vncserver -depth 24 -geometry 1280x800 :%i
ExecStop=/usr/local/bin/vncserver -kill :%i

[Install]
WantedBy=multi-user.target

Exit /etc/systemd/system/[email protected] and back in terminal

sudo systemctl daemon-reload
vncserver -kill :1
sudo systemctl enable [email protected]
sudo systemctl start vncserver@1
sudo systemctl status vncserver@1 # to check
sudo shutdown -r now

Installing Necessary Libraries and Programs

sudo -i
apt-get install chromium-browser
apt-get install curl 
apt-get install libcurl4-openssl-dev #needed for bioconductor
apt-get install libboost-iostreams-dev
apt-get install libgsl0-dev
apt-get install libmysql++-dev
apt-get install libboost-graph-dev
apt-get install libgl1-mesa-dev #for rgl
apt-get install libglu1-mesa-dev #for rgl
apt-get install libmysqlclient-dev #for R mysql
apt-get install libmpfr-dev
apt-get install libgmp-dev
apt-get install openmpi-bin 
apt-get install libopenmpi-dev
apt-get install ncbi-blast+ 
apt-get install ncbi-blast+-legacy
apt-get install mysql-client 
apt-get install mysql-server #password for root = Genomics
apt-get install libssl-dev
apt-get install libxml2-dev
apt-get install libxslt1-dev
apt-get install texlive-latex-extra 
apt-get install texlive-fonts-recommended
apt-get install dkms
apt-get install liblist-moreutils-perl 
apt-get install libstatistics-descriptive-perl
apt-get install libstatistics-r-perl 
apt-get install perl-doc 
apt-get install libtext-table-perl
apt-get install gdebi-core
apt-get install cmake
sudo apt-get install cython
apt-get install gedit gir1.2-gtksource-3.0
apt-get install emboss
apt install default-jdk
apt install openjdk-8-jdk
apt-get install ruby-dev nodejs
apt-get install python-pip python-numpy python-scipy
pip install --upgrade pip

Installing latest R

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'
apt-get update
apt-get install r-base
apt-get install r-base-dev

Installing Rstudio and make launcher

wget https://download1.rstudio.org/rstudio-xenial-1.1.463-amd64.deb
sudo gdebi rstudio-xenial-1.1.463-amd64.deb
sudo rm rstudio-xenial-1.1.463-amd64.deb

Installing R packages within Rstudio under /home/ubuntu/R/x86_64-pc-linux-gnu-library/3.5 [Default]

install.packages(c('swirl','ggplot2','genetics','hwde','seqinr','qtl','evaluate','formatR','highr','markdown','yaml','htmltools','caTools','bitops','knitr','rmarkdown','devtools','shiny','pvclust','gplots','cluster','igraph','scatterplot3d','ape','SNPassoc','rsconnect','dplyr','tidyverse','learnr'))
devtools::install_github(repo = "cran/PSMix")
source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite(c("Rsubread","snpStats","rtracklayer","goseq","impute","multtest","VariantAnnotation","chopsticks","edgeR"))
install.packages('LDheatmap')

Installing libre office

sudo apt-get install libreoffice-writer libreoffice-calc

Installing git viewer

sudo apt-get install gitg

Installing Jalview

sudo apt-get install jalview

Installing Others

sudo apt-get install seaview
sudo apt-get install clustalw clustalx kalign t-coffee muscle mafft probcons

Installing BWA

cd /usr/local/src
sudo git clone https://github.com/lh3/bwa.git
cd bwa; sudo make
cd /usr/local/bin
sudo ln -s /usr/local/src/bwa/bwa

Installing Bowtie

cd /usr/local/src
sudo wget https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.1.2/bowtie-1.1.2-linux-x86_64.zip
unzip bowtie-1.1.2-linux-x86_64.zip
cd /usr/local/bin
sudo ln -sf ../src/bowtie-1.1.2/bowtie .

Installing Bowtie2

cd /usr/local/src
wget sudo wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.5/bowtie2-2.3.5-linux-x86_64.zip
sudo unzip bowtie2-2.3.5-linux-x86_64.zip
cd /usr/local/bin
sudo cp -sf ../src/bowtie2-2.3.5-linux-x86_64/bowtie2 .

Installing Tophat

cd /usr/local/src
sudo wget https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz
sudo tar xvfz tophat-2.1.1.Linux_x86_64.tar.gz
cd /usr/local/bin
sudo ln -s ../src/tophat-2.1.1.Linux_x86_64/tophat .

Installing Samtools

cd /usr/local/src
sudo wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
sudo tar xvfj samtools-1.9.tar.bz2
cd samtools-1.9
sudo ./configure --prefix=/usr/local/src/samtools-1.9
sudo make
sudo make install
cd /usr/local/bin
sudo cp -s ../src/samtools-1.9/bin/samtools .

Installing Bedtools2

cd /usr/local/src
sudo wget https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools-2.28.0.tar.gz
sudo tar -zxvf bedtools-2.28.0.tar.gz
cd bedtools2
sudo make
cd /usr/local/bin
sudo cp -s /usr/local/src/bedtools2/bin/* .

Installing Fastqc

cd /usr/local/src
sudo wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.8.zip
sudo unzip fastqc_v0.11.8.zip
cd FastQC/
sudo chmod 0755 fastqc
cd /usr/local/bin
sudo cp -s ../src/FastQC/fastqc .

Installing seqtk

cd /usr/local/src
sudo git clone https://github.com/lh3/seqtk.git
cd seqtk
sudo make
cd /usr/local/bin
sudo ln -s /usr/local/src/seqtk/seqtk .

Installing Cufflinks

cd /usr/local/src
sudo wget http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz
sudo tar -xvzf cufflinks-2.2.1.Linux_x86_64.tar.gz
cd /usr/local/bin
sudo cp -sf ../src/cufflinks-2.2.1.Linux_x86_64/cuff* .
sudo cp -sf ../src/cufflinks-2.2.1.Linux_x86_64/g* .

Markdown viewer: Remarkable

sudo wget https://remarkableapp.github.io/files/remarkable_1.87_all.deb
sudo gdebi remarkable_1.87_all.deb

Installing MACS2

sudo pip install MACS2

Installing Cytoscape

cd /usr/local/src
sudo wget https://github.com/cytoscape/cytoscape/releases/download/3.7.1/Cytoscape_3_7_1_unix.sh
sudo chmod 755 Cytoscape_3_7_1_unix.sh
sudo ./Cytoscape_3_7_1_unix.sh

Installing FreeBayes

cd /usr/local/src
sudo git clone --recursive git://github.com/ekg/freebayes.git
cd freebayes
sudo make
sudo make install

Installing GATK 4.1.0.0

cd /usr/local/src
sudo wget https://github.com/broadinstitute/gatk/releases/download/4.1.0.0/gatk-4.1.0.0.zip
sudo unzip gatk-4.1.0.0.zip
cd /usr/local/bin
sudo ln -s /usr/local/src/gatk-4.1.0.0/gatk .

Installing Atom

sudo wget https://atom.io/download/deb
sudo mv deb atom.deb
sudo gdebi atom.deb

Add atom packages:

  • git-control
  • markdown-pdf
  • line-ending-converter
  • language-markdown
  • Sublime-Style-Column-Selection

In atom, go to preferences and diable the 'whitespace' package

Installing fish

sudo apt-get install fish

then

sudo vi /etc/passwd

And change the line for default shell to /usr/bin/fish, i.e.

ubuntu:x:1000:1000:Ubuntu:/home/ubuntu:/usr/bin/fish

sudo shutdown -r now

Nicer VIM colors

create ~/.vimrc and add

:color desert

Ensure encrypted VNC connection

Edit ~/.vnc/config and uncomment the SecurityTypes line:

securitytypes=vncauth,tlsvnc

fastStructure

cd /usr/local/src/
sudo git clone https://github.com/rajanil/fastStructure
cd /usr/local/src/fastStructure/
sudo git fetch
sudo git merge origin/master
sudo updatedb
sudo locate gsl_sf_psi.h
sudo locate libgslcblas.so
sudo locate libgsl.so
set -x LDFLAGS "-L/usr/lib/x86_64-linux-gnu"
set -x CFLAGS "-I/usr/include"
set -x LD_LIBRARY_PATH /usr/lib/x86_64-linux-gnu
cd vars
sudo python setup.py build_ext --inplace
cd ../
sudo python setup.py build_ext --inplace
cd /usr/local/bin
sudo nano fastStructure

add in following

#!/bin/bash
python /usr/local/src/fastStructure/structure.py

make executable

sudo chmod 755 fastStructure

igv

go to igv downloads and download the binary version (currently 2.5.0)

cd Downloads/
unzip IGV_Linux_2.5.0.zip 
sudo mv IGV_Linux_2.5.0/ /usr/local/src
sudo ln -s /usr/local/src/IGV_Linux_2.5.0/igv.sh /usr/local/bin

STAR

Download from https://github.com/alexdobin/STAR

cd /usr/local/src
sudo wget https://github.com/alexdobin/STAR/archive/2.7.0e.tar.gz
sudo tar -xzf 2.7.0e.tar.gz
cd /usr/local/bin
ln -s /usr/local/src/STAR-2.7.0e/bin/Linux_x86_64/STAR .

screenshooter

Add panel for screenshooter via the GUI

Updated class data

Used current public releases for C.elegan and D.melanogaster. Used Araport 11 for A.thaliana

Data used in the class can be downloaded here