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Setup.md

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Setup

All of the calculations and analyses are done in the iPython notebook. The code is written in Python and partially in R. The R is used to get data from GEO in a CEL file and process it to RNA-seq type data.

We recommend installing our Python virtual environment to perform the analysis. For detailed instructions, please refer to the “Preparation of the environment” section

Environment Requirements

  • Python 3.10
    • The packages are in requirements.txt
  • R 4.0.0 or higher
    • The packages are in install_R_packages.R
  • Jupyter notebook with its R and Python kernels
  • WSL (for Windows users)

WSL installation

If you are a Windows user, install WSL on your computer. If your operating system is Unix-based, skip this step.

To install WSL, follow the instructions provided on the WSL installation webpage.

Preparation of the environment

Please follow the instruction steps in the given order:

Installation of python using apt source

sudo apt-get update
sudo apt-get install python3.10-venv python3.10-dev python3-pip

Installation of python environment via pip

clone https://github.com/BostonGene/MFP
cd MFP
bash make_tme_environment.sh

make_tme_environment.sh creates python3.10 environment with all necessary packages and creates ipykernel core for the environment with name tme_env

Installation of python using conda

If you want to create a python environment via conda please follow this link

Install the jupyter kernel for your environment (for conda)

python -m ipykernel install --user --name=MFP_env

If your data is in CEL format you have to download R and all of the required packages.

Installation and preparation of R

sudo apt install r-base-core 
Rscript -e "install.packages('IRkernel')"
Rscript -e "IRkernel::installspec(user = FALSE)"
Rscript -e 'install.packages("httr", repos="http://cran.rstudio.com/")' 
Rscript -e 'install.packages("RJSONIO", repos="http://cran.rstudio.com/")' 
sudo apt-get install libxml2-dev libcurl4-openssl-dev libssl-dev
Rscript install_R_packages.R