Installation

Multi-platform (Docker)

Build a Docker image via

git clone https://github.com/BergmannLab/PascalX.git
cd PascalX
docker build . -t pascalx:latest

The image can be run in interactive mode with the host directory /your/workdir mounted as /data using the command

docker run --mount src=/your/workdir,target=/data,type=bind -p 8888:8888 -it pascalx bash

For data persistance after stopping the image, you should work exlusively in the /data directory.

A jupyter notebook running in the image can be started with

jupyter notebook --ip 0.0.0.0 --allow-root

Open on your host machine a browser and visit http://localhost:8888/ to use PascalX.

Note

You should allocate sufficient system resources to the docker runtime. A minimum of 8GB RAM should be made available. For making full use of parallel computation capabilities, at least 64GB of RAM is recommended. However, the precise numbers depend on the size of the GWAS and reference panel used.

Debian/Ubuntu

Use the Docker image or compile and install by yourself as follows:

Requirements:

  • Python3 with development headers

  • GNU g++ with libquadmath, make

  • BOOST libraries

Install of requirements (for sudoers):

sudo apt install python3 python3-dev python3-setuptools python3-pip g++ make libboost-all-dev

Set library path:

export LD_LIBRARY_PATH="/yourpath/PascalX/build/lib:$LD_LIBRARY_PATH"

Or, as sudoer, add to /etc/ld.so.conf.d/.

Install of PascalX:

git clone https://github.com/BergmannLab/PascalX.git
cd PascalX
make all
cd python
python3 setup.py install

Mac

As the default LLVM compiler used by Xcode does not support quadmath at the time being, we recommend to use Docker on MacOS.

Windows

Please use the Docker image.