Contents of Base Instance
- Free-tier Ubuntu 16.04 LTS AMI
- 2 Core, 4 Gb RAM
- 30Gb EBS storage
- Security, All TCP
- Elastic IP (Since been released)
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 –i
passwd ubuntu #"Genomics"
sudo apt install xfce4 xfce4-goodies tightvncserver
cd /usr/src
wget https://bintray.com/tigervnc/stable/download_file?file_path=tigervnc-1.7.0.x86_64.tar.gz
tar xvf download_file?file_path=tigervnc-1.7.0.x86_64.tar.gz
rm download_file?file_path=tigervnc-1.7.0.x86_64.tar.gz
cd /usr/bin
cp -s ../src/tigervnc-1.7.0.x86_64/usr/bin/* .
cd
exit
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
From new terminal window
ssh -L 5901:127.0.0.1:5901 -N -f -l ubuntu 52.52.160.9 #password = Genomics
Back in original terminal window
sudo vim ~/.config/xfce4/xfconf/xfce-perchannel-xml/xfce4-keyboard-shortcuts.xml
change
<property name="<Super>Tab" type="string" value="switch_window_key"/>
to
<property name="<Super>Tab" type="empty"/>
Fixes Tab so it autocompletes now
Make vnc a system service
sudo nano /etc/systemd/system/[email protected]
Pasted in the following
[Unit]
Description=Start TigerVNC server at startup
After=syslog.target network.target
[Service]
Type=forking
User=ubuntu
PAMName=login
PIDFile=/home/ubuntu/.vnc/%H:%i.pid
ExecStartPre=-/usr/bin/vncserver -kill :%i > /dev/null 2>&1
ExecStart=/usr/bin/vncserver -depth 24 -geometry 1280x800 :%i
ExecStop=/usr/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
nano .bashrc
## append 'cd /home/ubuntu' to end of file
cd
sudo -s
wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb
dpkg -i --force-depends google-chrome-stable_current_amd64.deb
apt-get install -f
rm google-chrome-stable_current_amd64.deb
### in Applications > Settings > Preferred Applications, set google chrome as browser
apt-get install curl 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 libopenmpi-dev
apt-get install ncbi-blast+ ncbi-blast+-legacy
apt-get install mysql-client 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 texlive-fonts-recommended
sudo apt-get install dkms
sudo apt-get install liblist-moreutils-perl libstatistics-descriptive-perl libstatistics-r-perl perl-doc libtext-table-perl
sudo apt-get install gdebi-core
sudo apt-get install cmake
echo 'deb https://cran.cnr.berkeley.edu/bin/linux/ubuntu xenial/' >> /etc/apt/sources.list
apt-get update
apt-get install r-base
apt-get install r-base-dev
sudo R
install.packages(c("swirl","ggplot2","genetics","hwde","GenABEL","seqinr","qtl")) ## mirror CA-1
source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite("chopsticks")
biocLite("edgeR")
biocLite("VariantAnnotation")
install.packages("LDheatmap")
Created a Desktop Launcher
wget https://download1.rstudio.org/rstudio-1.0.44-amd64.deb
sudo gdebi rstudio-1.0.44-amd64.deb
rm rstudio-1.0.44-amd64.deb
sudo apt-get install libreoffice-writer libreoffice-calc
sudo apt-get install gitg
sudo apt-get install htop
sudo apt-get install igv
sudo apt-get install jalview
sudo apt-get install seaview
sudo apt-get install clustalw clustalx kalign t-coffee muscle mafft probcons
cd /usr/src
git clone https://github.com/lh3/bwa.git
cd bwa; make
cd /usr/bin
ln -s /usr/src/bwa/bwa
cd /usr/src
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
rm bowtie-1.1.2-linux-x86_64.zip
cd /usr/bin
ln -sf ../src/bowtie-1.1.2/bowtie ./
cd /usr/src
wget https://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.9/bowtie2-2.2.9-linux-x86_64.zip
unzip bowtie2-2.2.9-linux-x86_64.zip
rm bowtie2-2.2.9-linux-x86_64.zip
cd /usr/bin
cp -sf ../src/bowtie2-2.2.9/bowtie2* ./
cd /usr/src
wget https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz
tar xvfz tophat-2.1.1.Linux_x86_64.tar.gz
rm tophat-2.1.1.Linux_x86_64.tar.gz
cd /usr/bin
ln -s /usr/src/tophat-2.1.1.Linux_x86_64/tophat* ./
cd /usr/src
wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2
tar -xvf samtools-1.3.1.tar.bz2
rm samtools-1.3.1.tar.bz2
cd samtools-1.3.1/
make
make prefix=/usr/src/samtools-1.3.1 install
cd /usr/bin
cp -s ../src/samtools-1.3.1/bin/* ./
cd /usr/src
wget https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz
tar -zxvf bedtools-2.25.0.tar.gz
rm bedtools-2.25.0.tar.gz
cd bedtools2
make
cd /usr/bin
cp -s /usr/src/bedtools2/bin/* ./
cd /usr/src
wget www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip
unzip fastqc_v0.11.5.zip
rm fastqc_v0.11.5.zip
cd FastQC/
chmod 0755 fastqc
cd /usr/bin
cp -s ../src/FastQC/fastqc ./
cd /usr/src
wget http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz
tar -xvzf cufflinks-2.2.1.Linux_x86_64.tar.gz
rm cufflinks-2.2.1.Linux_x86_64.tar.gz
cd /usr/bin
cp -sf ../src/cufflinks-2.2.1.Linux_x86_64/cuff* ./
cp -sf ../src/cufflinks-2.2.1.Linux_x86_64/g* ./
apt-get install blast2 ncbi-blast+ ncbi-blast+-legacy
wget https://remarkableapp.github.io/files/remarkable_1.87_all.deb
gdebi remarkable_1.87_all.deb
rm remarkable_1.87_all.deb
sudo apt-get install python-pip python-numpy python-scipy
sudo pip install --upgrade pip
sudo pip install MACS2
cd /usr/src
wget http://chianti.ucsd.edu/cytoscape-3.4.0/Cytoscape_3_4_0_unix.sh
sudo chmod 755 Cytoscape_3_4_0_unix.sh
sudo ./Cytoscape_3_4_0_unix.sh
Installed to default
sudo apt-get install gedit gir1.2-gtksource-3.0
sudo apt-get install emboss
wget https://mega.nz/linux/MEGAsync/xUbuntu_16.04/amd64/megasync-xUbuntu_16.04_amd64.deb
gdebi megasync-xUbuntu_16.04_amd64.deb
rm megasync-xUbuntu_16.04_amd64.deb
cd /
wget http://malooflab.phytonetworks.org/downloads/BIS180L/KorfData.tar.gz
tar xvf KorData.tar.gz
rm KorfData.tar.gz
sudo R
install.packages(c("evaluate","formatR","highr","markdown", "yaml","htmltools","caTools","bitops","knitr","rmarkdown"))
install.packages("devtools")
install.packages("shiny")
devtools::install_github("rstudio/shinyapps")
devtools::install_github(repo = "cran/PSMix")
install.packages(c("pvclust","gplots","cluster","igraph","scatterplot3d","ape","SNPassoc"))
source("http://bioconductor.org/biocLite.R")
biocLite(c("Rsubread","rtracklayer","goseq","impute","multtest","VariantAnnotation"))
cd /usr/src
git clone --recursive git://github.com/ekg/freebayes.git
cd freebayes
sudo make
sudo make install
Downloaded from website
cd /usr/src
mkdir GenomeAnalysisTK
mv ~/GenomeAnalysisTK-3.4-46.tar.bz2 /usr/src/GenomeAnalysisTK
cd GenomeAnalysisTK
bunzip2 GenomeAnalysisTK-3.6.tar.bz2
tar -xvf GenomeAnalysisTK-3.6.tar
cd /usr/bin
### created sh called GenomeAnalysisTK with chmod 755
### allows GenomeAnalysisTK to be invoked without including "java -jar /path/to/GenomeAnalysisTK.jar"
wget https://atom.io/download/deb
sudo gdebi deb
rm deb
Add atom packages:
- git-control
- markdown-pdf
- line-ending-converter
- language-markdown
- Sublime-Style-Column-Selection
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
May need to reboot for this to stick.
Change fish prompt with fish_config
Create file ~/.config/fish/fish.config and place a single line in it to ensure that fish starts in home directory:
cd /home/ubuntu
create ~/.vimrc and add
:color desert
Edit ``~/.vnc/config` and uncomment and edit the SecurityTypes line to be:
securitytypes=tlsvnc
Remove icons from desktop and instead add them to the dock. (left click on dock)
update apt-file and R
sudo apt-get update
sudo apt-get upgrade
echo 'deb https://cran.cnr.berkeley.edu/bin/linux/ubuntu xenial/' >> /etc/apt/sources.list # for some reason this was gone
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
apt-get update
apt-get upgrade
apt-get upgrade r-base-dev
update bioconductor
sudo R
source("https://bioconductor.org/biocLite.R")
biocLite()
q()
update packages that are in the user library
R
pkgs <- dir("~/R/x86_64-pc-linux-gnu-library/3.3")
install.packages(pkgs)
install.packages('rsconnect')
source("https://bioconductor.org/biocLite.R")
biocLite(c("goseq","PSMix","Rsubread","rtracklayer"))
Make system R library user modifiable (#normally not recommended)
sudo chown -R ubuntu /usr/local/lib/R
sudo chown -R root:root /data
sudo chmod 0755 /data
sudo apt-get install ruby-dev nodejs
sudo apt-get install cython
sudo -s
cd /usr/local/src/
sudo git clone https://github.com/rajanil/fastStructure
cd /usr/local/src/fastStructure/
git fetch
git merge origin/master
updatedb
locate gsl_sf_psi.h
locate libgslcblas.so
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
python setup.py build_ext --inplace
cd ../
python setup.py build_ext --inplace
alias "fastStructure" "python /usr/local/src/fastStructure/structure.py"
sudo apt-get remove igv #apt version is old and doesn't work well
go to igv downloads and download the binary version (currently 2.4.10) and igvtools (currently 2.3.98)
cd Downloads/
unzip IGV_2.4.10.zip
unzip igvtools_2.3.98.zip
sudo mv IGV_2.4.10/ /usr/local/src
sudo mv igvtools_2.3.98.zip /usr/local/src
sudo mv IGVTools/ /usr/local/src
sudo mv IGV_2.4.10.zip /usr/local/src
sudo ln -s /usr/local/src/IGV_2.4.10/igv.sh /usr/local/bin
sudo ln -s /usr/local/src/IGVTools/igvtools /usr/local/bin
sudo ln -s /usr/local/src/IGVTools/igvtools_gui /usr/local/bin
update launcher...
download from https://www.rstudio.com/products/rstudio/download/#download
cd Downloads
sudo gdebi rstudio-xenial-1.1.442-amd64\ \(1\).deb
sudo apt-get --purge remove megasync
Download from https://github.com/alexdobin/STAR/blob/master/bin/Linux_x86_64/STAR
cd Downloads/
chmod 0755 STAR
sudo mv STAR /usr/local/bin
Download from https://software.broadinstitute.org/gatk/download/; version 4.0.3.0
cd Downloads/
unzip gatk-4.0.3.0.zip
sudo mv gatk-4.0.3.0* /usr/local/src
sudo ln -s /usr/local/src/gatk-4.0.3.0/gatk /usr/local/bin/gatk
Add panel for screenshooter via the GUI
John's notes for fixing vncserver
Okay everything is all set. Tigervnc now runs on version 1.8. The problem most likely occurred due to the .pid file not being created in the ~/.vnc folder. Not sure why it was not created, but that was causing the startup process to fail. If the problem occurs again, this method worked for me. This manually created the .pid file for me allowing me kill the process. My suspicion is that changing the elastic ip address might have caused the issue.
vncserver -kill :1 # Failed so did the following
vncserver -depth 24 -geometry 1280x800 :1
sudo systemctl daemon-reload
sudo systemctl enable [email protected]
sudo systemctl start vncserver@1
sudo systemctl status vncserver@1 # Working