How to Install Sambamba on Linux
By Güngör Budak
- 2 minutes read - 276 wordsSambamba is a great utility to work with alignment file formats in bioinformatics such as BAM and CRAM. Follow below steps on any 64-bit Linux machine to install (this guide installs version 0.6.8
go to Sambamba releases page
for the most up-to-date version):
Create a softwares directory (optional but recommended)
cd ~/
mkdir softwares
cd softwares/
Download the static executable
wget https://github.com/biod/sambamba/releases/download/v0.6.8/sambamba-0.6.8-linux-static.gz
Unzip the package and rename the executable unpacked
gunzip sambamba-0.6.8-linux-static.gz
mv sambamba-0.6.8-linux-static.gz sambamba-0.6.8
Keeping version in the name, can be useful.
Change permissions to make it executable
chmod +x sambamba-0.6.8
Creating a symbolic link so you can call it anywhere
ln -s /opt/sambamba-0.6.8 /usr/local/bin
This step requires superuser permission, if you don’t have it just skip
Verify installation
sambamba-0.6.8 --version
sambamba 0.6.8 by Artem Tarasov and Pjotr Prins (C) 2012-2018
LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.4)
sambamba 0.6.8 by Artem Tarasov and Pjotr Prins (C) 2012-2018
LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.4)
or
./sambamba-0.6.8 --version
sambamba 0.6.8 by Artem Tarasov and Pjotr Prins (C) 2012-2018
LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.4)
sambamba 0.6.8 by Artem Tarasov and Pjotr Prins (C) 2012-2018
LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.4)
Notice the second verification is using ./
before executable which means it runs from the current working directory.
All in one line
wget https://github.com/biod/sambamba/releases/download/v0.6.8/sambamba-0.6.8-linux-static.gz && gunzip sambamba-0.6.8-linux-static.gz && mv /opt/sambamba-0.6.8-linux-static /opt/sambamba-0.6.8 && chmod +x /opt/sambamba-0.6.8 && ln -s /opt/sambamba-0.6.8 /usr/local/bin
Visit Sambamba GitHub page for more information.