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Installation Notes of Samtools

by Sheng Lian (20210818)

Introduction

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
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