Bolt-LMM

The BOLT-LMM algorithm computes statistics for testing association between phenotype and genotypes using a linear mixed model

Available from:

• https://storage.googleapis.com/broad-alkesgroup-public/BOLT-LMM/BOLT-LMM_manual.html

Latest source code may be downloaded from: https://alkesgroup.broadinstitute.org/BOLT-LMM/downloads/

To compile on Comet:

# Load the necessary modules
$ module load GCC/13.3.0
$ module load NLopt/2.10.0
$ module load LAPACK/3.12.1

# Download source
$ wget https://storage.googleapis.com/broad-alkesgroup-public/BOLT-LMM/downloads/BOLT-LMM_v2.5.tar.gz

# Unpack source archive
$ tar xfz BOLT-LMM_v2.5.tar.gz
$ cd BOLT-LMM_v2.5/src

# Edit Makefile to use GCC and link in additional runtime libraries
cat Makefile | \
	sed 's/CC\ \=\ icpc/#CC\ =\ icpc/g' | \
	sed 's/# CC = g++/CC = g++/g' | \
	sed 's/LLIBS = -lboost_program_options -lboost_iostreams -lzstd -lz -lnlopt/LLIBS = -lboost_program_options -lboost_iostreams -lzstd -lz -lnlopt -lblas -llapack/g'> Makefile.linux

# Compile source using modified Makefile
$ make -f Makefile.linux -j2

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