Table of Contents

• Using CoreMS with Docker Compose:
  • CoreMS Jupyter Notebook Docker Image
• Manual Installation
  • MAC
  • Windows

Using CoreMS Docker Image

This option is the easiest way to get a functional CoreMS, and Jupyter notebook working locally and uses docker-compose to set up the docker container, volumes, database, and virtual networks. If you choose this option you don't need to follow the manual installtion session.

• A custom python distribution with CoreMS and all dependencies installed
• A Jupyter notebook server with workflow example, and test data
• A PostgreSQL database for the molecular formulae library creation and search

The first step is to install docker. If you don't have docker installed yet, the easiest way is to install docker for desktop

1. Use git to clone the Day 3 tutorial repository into a location of your choice.

   git clone https://github.com/EMSL-Computing/Day3-EMSL-SummerSchool-2022

2. Copy your raw data into the day3-emsl-summerschool-2022/data/ directory before starting the services or :

   • modify the volume path in the docker-compose.yml file.

     • locate the volumes on docker-compose.yml (line 19):

     volumes:
     - ./data:/home/CoreMS/data
     

     • change ./data to your data directory path

3. Start the services using docker-compose:

   • save the file and then call:

   docker-compose up

4. On the terminal logs, find the Jupyter Notebook URL and copy and paste into your browser:

   corems | [I 05:41:37.790 NotebookApp]  or http://127.0.0.1:8888/?token=826ba2d4b2324f03441c189ddf4d1c84e365c39fb3377dd4
   
   

5. Open the Summer School CoreMS Tutorial notebook, and you are ready to go.

MAC Installation Instructions

1. Install Python 3.9.13 following this tutorial: https://www.chrisjmendez.com/2017/08/03/installing-multiple-versions-of-python-on-your-mac-using-homebrew/
   By the end of the tutorial, if you have not yet, set python 3.9.13 as the global option.
   If you are using Z shell, make sure to add the python path to your zprofile:

   $ echo 'eval "$(pyenv init --path)"' >> ~/.zprofile
   

2. Install git using brew

   $ brew install git
   

3. Install Commandline tools and GCC compilers:

   $ xcode-select –install
   $ brew install gcc
   

   Find the GCC version.

   $ cd usr/local/bin
   $ find gcc*  
   gcc-11  
   gcc-ar-11  
   gcc-nm-11  
   gcc-ranlib-11  
   

   In this case, the version is 11. So, replace the label {version} in the next step, and the command will be: "ls -s gcc-11 gcc"

   $ ln -s g++-{version} g++ 
   $ ln -s gcc-{version} gcc
   
   

   call gcc --version to check everything is working, and it should output something like:

   $ gcc --version
   gcc (Homebrew GCC 11.3.0_2) 11.3.0
   Copyright (C) 2021 Free Software Foundation, Inc.
   This is free software; see the source for copying conditions. There is NO
   warranty, not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
   

4. Install Mono and DotNet. This step is needed to install Python Net, which is used to read Thermo raw files.

   $ brew install pkg-config
   $ brew install mono-mdk
   $ brew install mono
   $ brew install dotnet
   

   At this point, you should have all the compilers and software framework needed to install corems

5. Go ahead and use git to clone the Day 3 tutorial repository into a location of your choice.

   $ git clone https://github.com/EMSL-Computing/Day3-EMSL-SummerSchool-2022
   

6. After the cloning process, go to the newly created repository directory and start a new python virtual environment, upgrade pip, install wheel and activate the new virtual environment:

   $ cd Day3-EMSL-SummerSchool-2002
   $ python -m venv venv
   $ python -m pip install -U pip
   $ python -m pip install wheel
   $ source venv/bin/activate
   

   Find the installed version of Mono:

   $ find /Library/Frameworks/ -name mono-2.pc
   
   /Library/Frameworks/Mono.framework/Versions/6.12.0/lib/pkgconfig/mono-2.pc
   

   Replace {mono version here} in the next step with the version found on the previous step, which is 6.12.0

   $PKG_CONFIG_PATH=/Library/Frameworks/Mono.framework/Versions/{mono version}/lib/pkgconfig/ python -m pip install pythonnet
   

7. Install CoreMS, CoreMS dependencies, and Jupyter

   $ python -m pip install -r requirements.txt
   

8. Run Jupyter Notebook

   jupyter notebook
   

This should open the browser with the Jupiter notebook, open the Summer School CoreMS Tutorial notebook, and you are ready to go.

Windows Installation Instructions

1. Download Microsoft Build Tools for Visual Studio 2022 https://aka.ms/vs/17/release/vs_BuildTools.exe
   • During the installation of C++ build tools and make sure the latest version for these:

   • MSVCv142 - VS 2022 C++ x64/x86 build tools
   • Windows 10 SDK

2. Download and install git:
   https://git-scm.com/download/

3. Download and install Python 3.9.13: https://www.python.org/downloads/

4. At this point, you should have all the compilers and software frameworks needed to install CoreMS. Go ahead and use git to clone the Day 3 tutorial repository into a location of your choice.

   $ git clone https://github.com/EMSL-Computing/Day3-EMSL-SummerSchool-2022
   

5. After the cloning process, go to the newly created repository directory and start a new python virtual environment, upgrade pip, install wheel and activate the new virtual environment:

   $ cd Day3-EMSL-SummerSchool-2002
   $ python3 -m venv venv
   $ python3 -m pip install -U pip
   $ python3 -m pip install -U setuptools
   $ python3 -m pip install wheel
   $  .\venv\Scripts\activate
   

6. Install CoreMS, CoreMS dependencies, and Jupyter

   $ python3 -m pip install -r requirements.txt
   

7. Run Jupyter Notebook

   jupyter notebook