Installation Notes of Samtools

by Sheng Lian (20210818)

Introduction

• Official Site: http://www.htslib.org/

Installation without root

• First install several libraries, e.g., zlib, bzip2, …

(Basically follow the instruction here.)

tar xvf samtools-1.13.tar.bz2
cd samtools-1.13
./configure --prefix=$HOME/usr
make
make install

• To solve the problem in ./configure results: ‘No such file or directory’ when installing bzip2:

• Download from SourceForge and tar -zxvf bzip2-1.0.6.tar.gz;

• Add Path (bzip2-1.0.6):

  export CPPFLAGS="-I$HOME/usr/include -I$HOME/bzip2-1.0.6"
  export LDFLAGS="-L$HOME/usr/lib -L$HOME/usr/lib64 -L$HOME/bzip2-1.0.6"
  export LD_LIBRARY_PATH=$HOME/usr/lib:$HOME/usr/lib64:$HOME/bzip2-1.0.6
  

Using Conda

• Install Miniconda:

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86_64.sh

• conda install -c bioconda samtools