Install samtools, bcftools and htslib on linux

install-samtools-bcftools-and-htslib.md

Install Samtools, BCFTools and htslib on linux

Install some build dependencies

sudo apt-get install autoconf automake make gcc perl zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev libncurses5-dev

samtools

$ wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2 -O samtools.tar.bz2
$ tar -xjvf samtools.tar.bz2
$ cd samtools-{version}
$ make
$ sudo make prefix=/usr/local/bin install
# if you have old version such as 0.x from samtools, you may remove it and create a link to new version
$ sudo apt remove samtools
$ sudo ln -s /usr/local/bin/bin/samtools /usr/bin/samtools
# Or, you can just use the path to call samtools
$ /usr/loca/bin/bin/samtools -h

BCFtools

$ wget https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2 -O bcftools.tar.bz2
$ tar -xjvf bcftools.tar.bz2
$ cd bcftools-{version}
$ make
$ sudo make prefix=/usr/local/bin install
$ sudo ln -s /usr/local/bin/bin/bcftools /usr/bin/bcftools

HTSlib

$ wget https://github.com/samtools/htslib/releases/download/1.3.2/htslib-1.3.2.tar.bz2 -O htslib.tar.bz2
$ tar -xjvf htslib.tar.bz2
$ cd htslib-{version}
$ make
$ sudo make install

@zsewa Your proposal worked perfectly. I was struggling with the installation of dependencies. I appreciate your contribution!

error in text: $ /usr/loca/bin/bin/samtools -h
should be: $ /usr/local/bin/bin/samtools -h

After I run this: $ sudo make prefix=/usr/local/bin install
I got result below. It might be run well. But when I call samtools --- Command 'samtools' not found, but can be installed with:
Please help me

mkdir -p -m 755 /usr/local/bin/bin /usr/local/bin/bin /usr/local/bin/share/man/man1
install -p samtools /usr/local/bin/bin
install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /usr/local/bin/bin
install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/fasta-sanitize.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-ampliconstats misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/wgsim_eval.pl misc/zoom2sam.pl /usr/local/bin/bin
install -p -m 644 doc/samtools*.1 misc/wgsim.1 /usr/local/bin/share/man/man1

Thank you very much!

@phancanhtrinh have you installed the dependencies?
Algo, I didn't understand why you needed to make the directories in the first row.
Could you post here all the commands you used?
You can algo install all these packages using conda