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=../htslibThese 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 zlib2) 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.gz3) 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'