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Minimac4 is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac/mininac2/minimac3.



See which versions are available:

$ module avail minimac4

Load one version into your environment and run it:

$ module load minimac4/1.0.3
$ minimac4


Notes from the sysadmin during installation.

$ cd /tmp
$ wget
$ 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