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

Hi ,

I'm trying to update my samtools (v0.1.18) to (v1.3.1), but got stuck here.

$ sudo make prefix=/usr/local/bin install

[sudo] password for biouser:

I've downloaded the Linux when I was in the RNASeq course before. I've tried to email them but the email was not sent. How can I proceed without typing in the password?

Thank you.

Hello Colleagues,

I tried to install SAMtools using above protocol but when I used command 'make' it gave me following error

bam_tview_curses.c:41:20: fatal error: curses.h: No such file or directory
compilation terminated.
Makefile:133: recipe for target 'bam_tview_curses.o' failed
make: *** [bam_tview_curses.o] Error 1

PLEASE GUIDE

@musohail1 You need to install ncurses. For example, on debian/ubuntu:
sudo apt-get install libncurses5-dev libncursesw5-dev

Hi adefelicibus,
thanks for the guide.

There are some typos in the install guide for samtools.
samtools is written as samtoos in some places.

Also consider adding the commands to install the build dependencies (according to https://github.com/samtools/samtools/blob/develop/INSTALL):

sudo apt-get update  # Ensure the package list is up to date
sudo apt-get install autoconf automake make gcc perl zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev libncurses5-dev

Altogether my propose for the samtools section would be:

$ sudo apt-get update && sudo apt-get install -y autoconf automake make gcc perl zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev libncurses5-dev
$ 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/local/bin/bin/samtools -h

Thanks and have a nice time

@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