How to build angsd on Hoffman2

Update April, 2021

qrsh -l rh7
git clone --recursive
git clone
cd htslib
git checkout 1.12
cd ../angsd
git checkout 0.935
make HTSSRC=../htslib

These instructions work for version 0.982 and were compiled on May, 2019:

1) get an interactive session and set the environment:

module load gcc/4.9.3    # or higher
module load xz
module load zlib

2) download and unpack the software (see also

3) make htslib first:

cd angsd/htslib
make CPPFLAGS='-I/u/local/apps/xz/5.2.3/include -I/u/local/apps/zlib/1.2.8/gcc-4.4.7/include' LDFLAGS='-L/u/local/apps/xz/5.2.3/lib -L/u/local/apps/zlib/1.2.8/gcc-4.4.7/lib'

4) now make angsd:

cd ../angsd
make HTSSRC=${HTSSRC}/ CPPFLAGS='-I${HTSSRC} -I/u/local/apps/xz/5.2.3/include -I/u/local/apps/zlib/1.2.8/gcc-4.4.7/include' LIBS='-L/u/local/apps/xz/5.2.3/lib -L/u/local/apps/zlib/1.2.8/gcc-4.4.7/lib -lz -lm -lbz2 -llzma -lpthread -lcurl -lcrypto ${HTSSRC}/libhts.a'

-- RD
Creation date: 5/11/2019 6:19 PM      Updated: 4/8/2021 5:25 PM