shiny server

shiny_server.sh

sudo sh -c 'echo "deb http://cran.rstudio.com/bin/linux/ubuntu trusty/" >> /etc/apt/sources.list'
gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
gpg -a --export E084DAB9 | sudo apt-key add -
sudo apt-get update
sudo apt-get -y install r-base libapparmor1 libcurl4-gnutls-dev libxml2-dev libssl-dev gdebi-core

sudo su - -c "R -e \"install.packages('shiny', repos = 'http://cran.rstudio.com/')\""
sudo su - -c "R -e \"install.packages('devtools', repos='http://cran.rstudio.com/')\""
sudo su - -c "R -e \"devtools::install_github('daattali/shinyjs')\""
sudo su - -c "R -e \"devtools::install_github('bioc/shinyjs')\""
sudo su - -c "R -e \"install.packages('rmarkdown', repos='http://cran.rstudio.com/')\""

wget https://download3.rstudio.org/ubuntu-12.04/x86_64/shiny-server-1.4.4.801-amd64.deb
wget https://download2.rstudio.org/rstudio-server-0.99.903-amd64.deb

sudo gdebi shiny-server-1.4.4.801-amd64.deb
sudo gdebi rstudio-server-0.99.903-amd64.deb
sudo reload shiny-server


sudo apt-get -y install fastqc python-stdeb python-pip python-dev
sudo apt-get -y install build-essentials

sudo pip install psutil
sudo pip install configobj
sudo apt-add-repository ppa:neufeldlab/ppa && sudo apt-get update && sudo apt-get -y install pandaseq

wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip
wget https://pypi.python.org/packages/15/a6/a05e99472b517aafd48824016f66458a31303f05256e9438ce9aec6b6bab/cutadapt-1.10.tar.gz#md5=74d3a41b46d44c2d0b3d66494264efb7
wget http://downloads.sourceforge.net/project/prinseq/standalone/prinseq-lite-0.20.4.tar.gz?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fprinseq%2Ffiles%2Fstandalone%2F&ts=1471227701&use_mirror=superb-sea2
mv prinseq-lite-0.20.4.tar.gz?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fprinseq%2Ffiles%2Fstandalone%2F prinseq-lite-0.20.4.tar.gz

wget http://vm-lux.embl.de/~kultima/share/MOCAT/v2.0/MOCAT2.zip
wget http://ab.inf.uni-tuebingen.de/data/software/megan6/download/MEGAN_Community_unix_6_4_21.sh
wget http://github.com/bbuchfink/diamond/releases/download/v0.8.18/diamond-linux64.tar.gz


tar xzf diamond-linux64.tar.gz
tar xzf prinseq-lite-0.20.4.tar.gz
tar xzf cutadapt-1.10.tar.gz
unzip Trimmomatic-0.36.zip
unzip MOCAT2.zip