st_aligner_bootstrap

Bootstrap: debootstrap
OSVersion: xenial
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
IncludeCmd: apt-get

%labels
Maintainer alexander.stuckey@scilifelab.se
Version 1.0

%environment
	SHELL=/bin/bash
	export SHELL

%post
	#----------------------
	#Install required tools
	#---------------------
	
	echo "deb http://archive.ubuntu.com/ubuntu xenial main multiverse universe restricted" >> /etc/apt/sources.list
	echo "deb http://archive.ubuntu.com/ubuntu xenial-updates main multiverse universe restricted" >> /etc/apt/sources.list
	echo "deb http://archive.ubuntu.com/ubuntu xenial-backports main multiverse universe restricted" >> /etc/apt/sources.list
	
	apt-get -y install software-properties-common

	add-apt-repository ppa:ubuntu-toolchain-r/test

	apt-get -y update
	apt-get -y upgrade
	apt-get -y install wget sudo
	apt-get -y install build-essential
	apt-get -y install gcc-7 g++-7
	apt-get -y install libboost-dev libboost-filesystem-dev libboost-program-options-dev libboost-system-dev libboost-thread-dev
	apt-get -y install git libgtk2.0-dev pkg-config ctags libavcodec-dev libavformat-dev libswscale-dev libboost-all-dev ctags
	apt-get -y install python-dev python-numpy libtbb2 libtbb-dev libjpeg-dev libpng-dev libtiff-dev libjasper-dev libdc1394-22-dev python-pip
	apt-get -y install npm
	pip install --upgrade pip
	pip install pandas
	apt-get -y install uwsgi uwsgi-core uwsgi-plugin-python
	rm /bin/sh
	ln -s /bin/bash /bin/sh
	
	mkdir tmppp
	cd tmppp
	wget https://cmake.org/files/v3.9/cmake-3.9.2.tar.gz
	tar -zxvf cmake-3.9.2.tar.gz
	cd cmake-3.9.2
	./bootstrap
	make
	make install

	update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-7 20
	update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-7 20
	update-alternatives --install /usr/bin/cc cc /usr/bin/gcc 30
	update-alternatives --set cc /usr/bin/gcc
	update-alternatives --install /usr/bin/c++ c++ /usr/bin/g++ 30
	update-alternatives --set c++ /usr/bin/g++

	update-alternatives --config gcc
	update-alternatives --config g++

	#----------------
	#Make home folder
	#----------------

	mkdir -p /home/st_aligner

	#--------------
	#Install opencv
	#--------------

	echo "Downloading and installing opencv 3.2.0"
	mkdir -p /github_dl
	cd /github_dl
	wget https://github.com/opencv/opencv/archive/3.2.0.tar.gz
	tar -zxvf 3.2.0.tar.gz
	cd opencv-3.2.0
	mkdir -p build
	cd build
	cmake -D CMAKE_BUILD_TYPE=Release -D CMAKE_INSTALL_PREFIX=/usr/local ..
	make -j2
	sudo make install	

	#----------------------------------
	#Install tissue recognition library
	#----------------------------------

	echo "Installing tissue recognition library"
	cd /github_dl
	git clone https://github.com/SpatialTranscriptomicsResearch/tissue_recognition
	cd tissue_recognition
	mkdir -p build
	cd build
	cmake ..
	make install
	pip install setuptools
	cd ../python-module
	python setup.py install
	
	#------------------
	#Install st aligner
	#------------------

	echo "Installing st_aligner"
	cd /github_dl
	git clone https://github.com/SpatialTranscriptomicsResearch/st_aligner.git
	cd st_aligner
	pip install -r server/requirements.txt
	pip install virtualenv
	virtualenv /home/st_aligner/venv
	. /home/st_aligner/venv/bin/activate
	pip install -r server/requirements.txt
	sed -i '/chdir/c\chdir = /home/st_aligner/server' /github_dl/st_aligner/server/uwsgi-server-config.ini
	sed -i '/logto/c\logto = /home/st_aligner/server/logs/%n.log' /github_dl/st_aligner/server/uwsgi-server-config.ini
	sed -i '/plugin/c\plugin = /usr/lib/uwsgi/plugins/python_plugin.so' /github_dl/st_aligner/server/uwsgi-server-config.ini
	sed -i '/virtualenv/c\virtualenv = /home/st_aligner/venv' /github_dl/st_aligner/server/uwsgi-server-config.ini
	sed -i '/static-map/c\static-map = /=/home/st_aligner/client' /github_dl/st_aligner/server/uwsgi-server-config.ini
	sudo cp server/uwsgi-server-config.ini /etc/uwsgi/apps-available/
	sudo ln -s /etc/uwsgi/apps-available/uwsgi-server-config.ini /etc/uwsgi/apps-enabled/uwsgi-server-config.ini
	cd /github_dl/st_aligner/client
	npm install
	ln -s /usr/bin/nodejs /usr/bin/node
	make DEVEL=1

	#--------------------------------
	#Set up folders to run st_aligner
	#--------------------------------

	cp -R /github_dl/st_aligner/server /home/st_aligner/server
	cp -R /github_dl/st_aligner/client /home/st_aligner/client
	mv /home/st_aligner/server/utils.py /home/st_aligner/server/utility.py
	cp -R /github_dl/tissue_recognition/python-module/tissue_recognition/*.py /home/st_aligner/server
	cp /github_dl/tissue_recognition/build/src/*.so /home/st_aligner/server
	cp /github_dl/opencv-3.2.0/build/lib/libopencv_core.so.3.2 /home/st_aligner/server
	cp /github_dl/opencv-3.2.0/build/lib/libopencv_imgproc.so.3.2 /home/st_aligner/server
	mkdir -p /home/st_aligner/server/logs
	ln -s /home/st_aligner/client /home/st_aligner/server/client

	#-------------------------------
	#Add coordinate adjusting script
	#-------------------------------
	cd /home/st_aligner
	wget https://rawgit.com/Alexander-Stuckey/st_pipeline/master/scripts/adjust_matrix_coordinates.py
		
	#----------------------------
	#Edit scripts to work locally
	#----------------------------
	
	chmod -R 0777 /home/st_aligner/
	cd /home/st_aligner/server
	sed -i 's/utils/utility/g' server.py
	sed -i 's@../client/devel@client/devel@g' server.py
	sed -i 's/from . import utils/import utils/' tissue_recognition.py
	sed -i '9,11d' tissue_recognition.py
	sed -i 's@LIB_FILE@"/home/st_aligner/server/libtissue-recognition.so"@' tissue_recognition.py

	#--------
	#Clean up
	#--------

	rm /github_dl/*.tar.gz
	exit 0
	
%runscript

	echo "Starting uwsgi webserver..."
	cd /home/st_aligner
	uwsgi server/uwsgi-server-config.ini