tecdatalab - BioStructure Project

-> EvoSeg: An evolutionary automatic subunit segmentation

EvoSeg is a tool for automatic subunit segmentation of EM Maps.

Tutorial (Jupyter Noteboook)

-> Project download and configuration

1) Clone the repository on your local machine

git clone https://github.com/tecdatalab/biostructure.git

2) Install all the dependencies

Two options avaible:

2.1) Fast Installation Script

./installation_script.sh

2.2) Steb by Step Installation

• Node JS installation

Step 1 - Install cURL

sudo apt install curl

Step 2 - Add Node JS PPA

curl -sL https://deb.nodesource.com/setup_10.x | sudo bash -

Step 3 - Install Node JS

sudo apt install nodejs

Step 4 - Install npm

sudo apt-get install -y npm

• Express API installation

Step 1 - Change directory to backend

cd backend

Step 2 - Install node packages

npm install

Step 3 - Run API

node src/index.js [database username] [database password] [host] [port] [database name]

• Angular installation

Step 1 - Change directory to emsurfer

cd emsurfer

Step 2 - Install node packages

npm install

Step 3 - Link angular/cli to npm

sudo npm link @angular/cli

Step 4 - Run Angular

ng serve

• Updater installation

Step 1 - Update packages

sudo apt-get update && sudo apt-get upgrade

Step 2 - Install Python 3.6

sudo apt-get install python3.6

Step 3 - Install Pip3

echo Y | sudo apt-get install python3-pip

Step 4 - Install Tkinter

echo Y | sudo apt-get install python3-tk 

Step 5 - Install OpenGL

echo Y | sudo apt-get install libglfw3-dev

Step 6 - Install Libpq-dev python-dev

sudo apt-get install libpq-dev python-dev

Step 7 - Install Psycopg2

sudo pip3 install -U psycopg2

Step 8 - Install Numpy

sudo pip3 install -U numpy 

Step 9 - Install Biopandas

sudo pip3 install -U biopandas 

Step 10 - Install Cython

sudo pip3 install -U Cython 

Step 11 - Install Pandas

sudo pip3 install -U pandas

Step 12 - Install Sklearn

sudo pip3 install -U sklearn

Step 13 - Install Triangle

sudo pip3 install -U triangle

Step 14 - Install Scipy

sudo pip3 install -U scipy

Step 15 - Install Matplotlib

sudo pip3 install -U matplotlib

Step 16 - Install Scikit-image

sudo pip3 install -U scikit-image

Step 17 - Install Glumpy

sudo pip3 install -U glumpy

Step 18 - Install Pyopengl

sudo pip3 install -U pyopengl

Step 19 - Install Packaging

sudo pip3 install -U packaging 

Step 20 - Install Appdirs

sudo pip3 install -U appdirs  

Step 21 - Install Glfw

sudo pip3 install -U glfw 

Step 22 - Install Pyqt5

sudo pip3 install -U pyqt5

Step 23 - Install Psycopg2-binary

sudo pip3 install -U psycopg2-binary

Step 24 - Install Requests

sudo pip3 install -U requests

Step 25 - Install clint

sudo pip3 install -U clint

Step 26 - Install psutil

sudo pip3 install -U psutil

Step 27 - Permissions of execution to em_volume

chmod +x db/Updater/generators/em_volume

Step 28 - Permissions of execution to map2zernike

chmod +x db/Updater/generators/map2zernike

Step 29 - Change directory to Main file

cd biostructure/db/Updater/updater/

Step 30 - Run Updater

python3.6 Main.py [log] [initialEMD] [mode] [image] [descriptor]

-> Run Project

./init

This start the back-end server & the fornt-end webpage

-> Contributors