How to build angsd on Hoffman2

Update April, 2021

qrsh -l rh7
git clone --recursive https://github.com/samtools/htslib.git

git clone https://github.com/ANGSD/angsd.git 

cd htslib

git checkout 1.12

make

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:

qrsh 


module load gcc/4.9.3    # or higher


module load xz
module load zlib

2) download and unpack the software (see also http://www.popgen.dk/angsd/index.php/Installation):

wget http://popgen.dk/software/download/angsd/angsd0.928.tar.gz

tar xvf angsd0.928.tar.gz

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:

HTSSRC=`pwd`
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

angsd angsd htslib htslib

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