minimac4-software
Table of Contents
minimac4
Minimac4 is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac/mininac2/minimac3.
Information
- Version: 1.0.3
- Added: June, 2022
Usage
See which versions are available:
$ module avail minimac4
Load one version into your environment and run it:
$ module load minimac4/1.0.3 $ minimac4
Installation
Notes from the sysadmin during installation.
$ cd /tmp $ wget https://github.com/statgen/Minimac4/archive/refs/tags/v1.0.3.tar.gz $ tar xf v1.0.3.tar.gz $ cd Minimac4-1.0.3 $ sudo mkdir -p /export/apps/minimac4/1.0.3/bin $ sudo chown aorth:aorth /export/apps/minimac4/1.0.3 $ python3 -m venv venv $ source venv/bin/activate $ pip install --upgrade setuptools pip wheel $ pip install cget $ cget install -f ./requirements.txt $ mkdir build && cd build $ cmake -DCMAKE_TOOLCHAIN_FILE=../cget/cget/cget.cmake .. $ make $ cmake -DCMAKE_INSTALL_PREFIX=/export/apps/minimac4/1.0.3 -P cmake_install.cmake $ sudo chown -R root:root /export/apps/minimac4/1.0.3
The build system uses cget to pull down a few C++ dependencies like zlib. It's unclear whether we need to have those available at runtime or not. The resulting binary seems to run fine without any environment variables.
minimac4-software.txt · Last modified: 2022/06/17 07:16 by aorth