ILRI Research Computing

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====== 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
  * Link: https://github.com/statgen/Minimac4

===== Usage =====

See which versions are available:
<code>$ module avail minimac4</code>

Load one version into your environment and run it:
<code>$ module load minimac4/1.0.3
$ minimac4</code>

===== Installation ======
Notes from the sysadmin during installation.

<code>$ 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</code>

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.