git clone https://github.com/ANGSD/angsd/; cd angsd; make
This will build angsd using the htslib submodule.
After building it, you can use realpath angsd to obtain the realpath to the angsd executable.
$ realpath angsd
/home/example/path/angsd/angsd
Use this path to replace all angsd commands in your script to make sure you are using the correct version. If you are using any utilities make sure you use the fullpath for them, too.
For example, replace
angsd -out out -doMajorMinor 1 -doMaf 3 -bam bam.filelist -GL 2
realSFS pop1.saf.idx pop2.saf.idx
with
/home/example/path/angsd/angsd -out out -doMajorMinor 1 -doMaf 3 -bam bam.filelist -GL 2
/home/example/path/angsd/misc/realSFS pop1.saf.idx pop2.saf.idx