setup_install.sh

sudo apt install mysql-server
sudo apt-get install ubuntu-restricted-extras med-bio

#qt5
sudo apt install qt5-default
sudo apt-get install qtdeclarative5-dev qml-module-qtquick-controls
qttools5-dev libqt5x11extras5-dev qtbase5-dev

sudo apt-get install ubuntu-restricted-extras med-bio
sudo apt-get install byobu vim firefox smplayer pidgin quiterss hexchat sshfs git htop indicator-multiload shutter virtualenvwrapper python3-dev python3-pip amarok spyder thunderbird kile 


#java8
sudo add-apt-repository ppa:webupd8team/java
#change vivid to utopic
sudo apt-get update
sudo apt-get install oracle-java9-installer

sudo apt-get install python-pip virtualenvwrapper

wget https://download1.rstudio.org/rstudio-xenial-1.0.153-amd64.deb
sudo dpkg -i rstudio-xenial-1.0.153-amd64.deb
sudo apt -f install
sudo apt install r-base r-base-dev


#variety
sudo add-apt-repository ppa:peterlevi/ppa
sudo apt-get update
sudo apt-get install variety variety-slideshow

sudo add-apt-repository ppa:fyrmir/livewallpaper-daily
sudo apt-get update && sudo apt-get install livewallpaper

#purple-facebook
sudo sh -c "echo 'deb http://download.opensuse.org/repositories/home:/jgeboski/xUbuntu_16.04/ /' >> /etc/apt/sources.list.d/jgeboski.list"
cd /tmp && wget  http://download.opensuse.org/repositories/home:/jgeboski/xUbuntu_16.04/Release.key
sudo apt-key add - < Release.key  
sudo apt-get update
sudo apt-get install purple-facebook


# add biolinux packages
sudo apt install bamtools bio-rainbow biomaj biomaj-watcher biomaj3-commons bioperl clearcut emboss-explorer fastahack fastml fsm-lite grinder harvest-tools kmc kraken libbamtools-dev libbamtools-doc libbamtools2.4.0 libbio-coordinate-perl libbio-eutilities-perl libbio-perl-perl libbio-perl-run-perl libbiococoa-dev libbiococoa2 libbiod-dev libbiod0 libbiojava-java libbiojava4-java libbpp-core-dev libbpp-core3 libbpp-phyl-dev libbpp-phyl-omics-dev libbpp-phyl-omics2 libbpp-phyl11 libbpp-popgen-dev libbpp-popgen7 libbpp-qt-dev libbpp-qt1 libbpp-seq-dev libbpp-seq-omics-dev libbpp-seq-omics2 libbpp-seq11 libcdk-java libfastahack-dev libfastahack0 libgenome-1.3-0v5 libgenome-1.3-dev libgenometools0 libgenometools0-dev libjebl2-java libjebl2-java-doc libjloda-java libkmc-dev libncl-dev libncl1 libqes-dev libqes0 libshogun-dbg libshogun-dev libshogun16 libswiss-perl libtfbs-perl mapsembler2 med-bio med-bio-dev med-cloud microbegps mobyle mobyle-tutorials mobyle-utils mothur mothur-mpi ncl-tools poa python-biomaj3 python-biopython python-biotools python-csb python-csb-doc python-genometools python-pbcore python-pbcore-doc python-pyvcf python-pyvcf-examples python-ruffus python-shogun python-shogun-dbg python-skbio-doc python-xopen python3-biomaj3 python3-biopython python3-biotools python3-csb python3-pybedtools python3-pyvcf python3-ruffus python3-skbio python3-xopen pyvcf r-bioc-biomart r-bioc-hilbertvis radiant ruby-bio shogun-cmdline-static shogun-doc-cn shogun-doc-en sickle smrtanalysis smrtanalysis-dev snakemake tophat ugene ugene-data velvet velvet-example velvet-long velvet-tests 

#install mendelmd
git clone git@github.com:raonyguimaraes/mendelmd.git
sudo apt install docker-compose
sudo usermod -aG docker $(whoami)
exec sudo su ${USER}
docker-compose up

sudo sh -c 'echo "deb http://apt.postgresql.org/pub/repos/apt/ $(lsb_release -cs)-pgdg main" > /etc/apt/sources.list.d/pgdg.list'
sudo apt install pgadmin4