How To Install samtools on Fedora 34
Introduction
In this tutorial we learn how to install samtools on Fedora 34.
What is samtools
SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
We can use yum or dnf to install samtools on Fedora 34. In this tutorial we discuss both methods but you only need to choose one of method to install samtools.
Install samtools on Fedora 34 Using dnf
Update yum database with dnf using the following command.
sudo dnf makecache --refresh
The output should look something like this:
Fedora 34 - x86_64 20 kB/s | 6.6 kB 00:00
Fedora 34 openh264 (From Cisco) - x86_64 1.4 kB/s | 989 B 00:00
Fedora Modular 34 - x86_64 68 kB/s | 6.5 kB 00:00
Fedora 34 - x86_64 - Updates 3.5 kB/s | 6.2 kB 00:01
Fedora Modular 34 - x86_64 - Updates 17 kB/s | 5.9 kB 00:00
Metadata cache created.
After updating yum database, We can install samtools using dnf by running the following command:
sudo dnf -y install samtools
Install samtools on Fedora 34 Using yum
Update yum database with yum using the following command.
sudo yum makecache --refresh
The output should look something like this:
Fedora 34 - x86_64 20 kB/s | 6.6 kB 00:00
Fedora 34 openh264 (From Cisco) - x86_64 1.4 kB/s | 989 B 00:00
Fedora Modular 34 - x86_64 68 kB/s | 6.5 kB 00:00
Fedora 34 - x86_64 - Updates 3.5 kB/s | 6.2 kB 00:01
Fedora Modular 34 - x86_64 - Updates 17 kB/s | 5.9 kB 00:00
Metadata cache created.
After updating yum database, We can install samtools using yum by running the following command:
sudo yum -y install samtools
How To Uninstall samtools on Fedora 34
To uninstall only the samtools package we can use the following command:
sudo dnf remove samtools
samtools Package Contents on Fedora 34
/usr/bin/ace2sam
/usr/bin/blast2sam.pl
/usr/bin/bowtie2sam.pl
/usr/bin/export2sam.pl
/usr/bin/interpolate_sam.pl
/usr/bin/maq2sam-long
/usr/bin/maq2sam-short
/usr/bin/md5fa
/usr/bin/md5sum-lite
/usr/bin/novo2sam.pl
/usr/bin/plot-bamstats
/usr/bin/psl2sam.pl
/usr/bin/sam2vcf.pl
/usr/bin/samtools
/usr/bin/samtools.pl
/usr/bin/seq_cache_populate.pl
/usr/bin/soap2sam.pl
/usr/bin/wgsim
/usr/bin/wgsim_eval.pl
/usr/bin/zoom2sam.pl
/usr/lib/.build-id
/usr/lib/.build-id/17
/usr/lib/.build-id/17/03d516875653025bbf1008117952e3e0b33d26
/usr/lib/.build-id/81
/usr/lib/.build-id/81/e8602a59ef7b6769a20981b47a512fea04a6b6
/usr/lib/.build-id/84
/usr/lib/.build-id/84/1bedb2766137ed5f188e60283362f9a8327664
/usr/lib/.build-id/8f
/usr/lib/.build-id/8f/49a3e8c70a662814042d61e259b0a15a1de21b
/usr/lib/.build-id/99
/usr/lib/.build-id/99/89cf99cb22737f640b08117d649c4db8e489c4
/usr/lib/.build-id/ac
/usr/lib/.build-id/ac/74a5327175388cb5f0fa3c40d7d449813c053f
/usr/lib/.build-id/b6
/usr/lib/.build-id/b6/337478ad75d2326f90b9f5a11b20c716da4602
/usr/share/doc/samtools
/usr/share/doc/samtools/AUTHORS
/usr/share/doc/samtools/ChangeLog.old
/usr/share/doc/samtools/NEWS
/usr/share/doc/samtools/examples
/usr/share/doc/samtools/examples/00README.txt
/usr/share/doc/samtools/examples/ex1.fa
/usr/share/doc/samtools/examples/ex1.sam.gz
/usr/share/doc/samtools/examples/toy.fa
/usr/share/doc/samtools/examples/toy.sam
/usr/share/licenses/samtools
/usr/share/licenses/samtools/LICENSE
/usr/share/man/man1/samtools.1.gz
/usr/share/man/man1/wgsim.1.gz
References
Summary
In this tutorial we learn how to install samtools on Fedora 34 using yum and dnf.