Minor points on installation

[jinghuazhao]

Dear ANGSD team,

I am pleased to get the package up and running. I would like to mention a few minor points:

1. I felt puzzled that my initial script was not working

wget -qO- https://github.com/ANGSD/angsd/releases/download/0.940/angsd0.940.tar.gz | tar xfz-

until I realised that the tar.gz file is simply a tar file, so tar xf - is appropriate. I am sure users must have already followed tar xf - as documented.

2. I have already had htslib/1.20 module on our system, so HTSSRC=systemwide can point to that; I found that we can get around the missing htslib issue as follows (here CEUADMIN=/usr/local/Cluster-Apps/ceuadmin/),

wget -qO- https://github.com/ANGSD/angsd/archive/refs/tags/0.940.tar.gz | tar xfz -
cd angsd-0.940/
export CPATH=$CEUADMIN/htslib/1.20/include:$CPATH
make HTSSRC=$CEUADMIN/htslib/1.20/lib install prefix=$CEUADMIN/angsd/0.940
make clean

noting that Git release is a tar.gz, with a somewhat unusual CPATH option being ready to help, and the prefix= option comes handy (everything can be done in one go)..

3. docker/singularity

I am using a shared HPC where docker is not up systemwide by default but singularity is available.

I have noted these here, https://cambridge-ceu.github.io/csd3/applications/angsd.html; I am less confident with the test implemented there, so do warn me if anything is drastically wrong.

Best regards,

JIng Hua