Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04

13 months ago by

otwtgin2010 • 200

otwtgin2010 • 200 wrote:

Just thought I would contribute this since figuring it all out was a super confusing process consisting of a few hundred google searches. It's likely it was just me, but maybe there are a few other people like me who will benefit from being able to avoid the process. This was a clean Ubuntu 18.04 install. Probably most people do not have that luxury.

Install Updates and Required Packages

sudo apt-get update
sudo apt-get install gcc
sudo apt-get install make
sudo apt-get install libbz2-dev
sudo apt-get install zlib1g-dev
sudo apt-get install libncurses5-dev 
sudo apt-get install libncursesw5-dev
sudo apt-get install liblzma-dev

Install HTSLIB

cd /usr/bin
wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2
tar -vxjf htslib-1.9.tar.bz2
cd htslib-1.9
make

Install SAMTOOLS

cd ..
wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
tar -vxjf samtools-1.9.tar.bz2
cd samtools-1.9
make

Install BCFTools

cd ..
wget https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2
tar -vxjf bcftools-1.9.tar.bz2
cd bcftools-1.9
make

Export To Path And Refresh

export PATH="$PATH:/usr/bin/bcftools-1.9"
export PATH="$PATH:/usr/bin/samtools-1.9"
export PATH="$PATH:/usr/bin/htslib-1.9"
source ~/.profile

htslib bcftools tutorial samtools • 11k views

ADD COMMENT • link •

written 13 months ago by otwtgin2010 • 200

Thank you otwtgin2010 for the work. Others may benefit from it, if they want to compile these softwares from source. Another option would be to use the Anaconda package manager. With conda, things are as easy as conda install -c bioconda samtools, taking care of the dependencies internally.

ADD REPLY • link written 13 months ago by ATpoint ♦ 21k

This is the best way to go about it, IMO. Neither apt-get nor brew allow creating environments.

ADD REPLY • link written 13 months ago by RamRS ♦ 23k

+1 for sharing your experiences with other users. Keep on contributing!

As Ram said, in this case one should follow the instruction given by the authors of the program.

fin swimmer

ADD REPLY • link written 13 months ago by finswimmer ♦ 12k

this was super helpful for my attempt to get HTSlib working

ADD REPLY • link written 5 months ago by MaxF • 10

That was an extremely helpful walk-through. I've been trying to install BCFtools following their guidelines, but failing miserably (the operation would stop due to not finding curl:curl.h directory). Now, it has worked just fine.

And sorry for the lay question - I am still taking slow steps in learning Unix - but what is the meaning of the last step, "export to path and refresh"? I tried looking on the export --help, but I am still quite not sure what it does.

Many thanks, @otwtgin2010 !

ADD REPLY • link written 26 days ago by dodausp • 110

It means that you have to put the folder where the executable is in into your .bashrc or .bash_profile like

export PATH=$PATH:/path/to/folder/with/executable

Still, it would be easier to use a package manager such as conda.

ADD REPLY • link modified 26 days ago • written 26 days ago by ATpoint ♦ 21k

mkdir ~/myBinaries/ cd ~/myBinaries/ find /usr/bin/bcftools-1.9/ -type f -executable | xargs -I v_b ln -s v_b ./ find /usr/bin/samtools-1.9/ -type f -executable | xargs -I v_b ln -s v_b ./ find /usr/bin/htslib-1.9/ -type f -executable | xargs -I v_b ln -s v_b ./ cd - echo 'export PATH=$PATH:~/myBinaries' >>~/.profile source ~/.profile

Install Updates and Required Packages

Install HTSLIB

Install SAMTOOLS

Install BCFTools

Export To Path And Refresh

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