How To Install htslib on CentOS 8
Introduction
In this tutorial we learn how to install htslib on CentOS 8.
What is htslib
HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools.
We can use yum or dnf to install htslib on CentOS 8. In this tutorial we discuss both methods but you only need to choose one of method to install htslib.
Install htslib on CentOS 8 Using dnf
Update yum database with dnf using the following command.
sudo dnf makecache --refresh
The output should look something like this:
CentOS Linux 8 - AppStream 43 kB/s | 4.3 kB 00:00
CentOS Linux 8 - BaseOS 65 kB/s | 3.9 kB 00:00
CentOS Linux 8 - ContinuousRelease 43 kB/s | 3.0 kB 00:00
CentOS Linux 8 - Extras 23 kB/s | 1.5 kB 00:00
CentOS Linux 8 - FastTrack 40 kB/s | 3.0 kB 00:00
CentOS Linux 8 - HighAvailability 36 kB/s | 3.9 kB 00:00
CentOS Linux 8 - Plus 24 kB/s | 1.5 kB 00:00
CentOS Linux 8 - PowerTools 50 kB/s | 4.3 kB 00:00
Extra Packages for Enterprise Linux Modular 8 - x86_64 13 kB/s | 9.2 kB 00:00
Extra Packages for Enterprise Linux 8 - x86_64 24 kB/s | 8.5 kB 00:00
Metadata cache created.
After updating yum database, We can install htslib using dnf by running the following command:
sudo dnf -y install htslib
Install htslib on CentOS 8 Using yum
Update yum database with yum using the following command.
sudo yum makecache --refresh
The output should look something like this:
CentOS Linux 8 - AppStream 43 kB/s | 4.3 kB 00:00
CentOS Linux 8 - BaseOS 65 kB/s | 3.9 kB 00:00
CentOS Linux 8 - ContinuousRelease 43 kB/s | 3.0 kB 00:00
CentOS Linux 8 - Extras 23 kB/s | 1.5 kB 00:00
CentOS Linux 8 - FastTrack 40 kB/s | 3.0 kB 00:00
CentOS Linux 8 - HighAvailability 36 kB/s | 3.9 kB 00:00
CentOS Linux 8 - Plus 24 kB/s | 1.5 kB 00:00
CentOS Linux 8 - PowerTools 50 kB/s | 4.3 kB 00:00
Extra Packages for Enterprise Linux Modular 8 - x86_64 13 kB/s | 9.2 kB 00:00
Extra Packages for Enterprise Linux 8 - x86_64 24 kB/s | 8.5 kB 00:00
Metadata cache created.
After updating yum database, We can install htslib using yum by running the following command:
sudo yum -y install htslib
How To Uninstall htslib on CentOS 8
To uninstall only the htslib package we can use the following command:
sudo dnf remove htslib
htslib Package Contents on CentOS 8
/usr/lib/.build-id
/usr/lib/.build-id/0d
/usr/lib/.build-id/0d/c346908322b4b9417d4d8253eb94896af6340a
/usr/lib/.build-id/27
/usr/lib/.build-id/27/6240cafb17d8e040915181db330d8be410405e
/usr/lib/.build-id/44
/usr/lib/.build-id/44/5dd6fee7a43ad97f39327d5341f87c2dfa5f65
/usr/lib/.build-id/56
/usr/lib/.build-id/56/5a8b41e9bc728076f1984a91b53d69ac72cf4f
/usr/lib64/libhts.so.1.9
/usr/lib64/libhts.so.2
/usr/libexec/htslib
/usr/libexec/htslib/hfile_gcs.so
/usr/libexec/htslib/hfile_libcurl.so
/usr/libexec/htslib/hfile_s3.so
/usr/share/doc/htslib
/usr/share/doc/htslib/NEWS
/usr/share/licenses/htslib
/usr/share/licenses/htslib/LICENSE
/usr/share/man/man5/faidx.5.gz
/usr/share/man/man5/sam.5.gz
/usr/share/man/man5/vcf.5.gz
References
Summary
In this tutorial we learn how to install htslib on CentOS 8 using yum and dnf.