How To Install mmseq on Fedora 34

mmseq is Haplotype and isoform specific expression estimation for RNA-seq

Introduction

In this tutorial we learn how to install mmseq on Fedora 34.

What is mmseq

Software for fast, scalable haplotype and isoform expression estimation using multi-mapping RNA-seq reads. Example scripts are included.

We can use yum or dnf to install mmseq on Fedora 34. In this tutorial we discuss both methods but you only need to choose one of method to install mmseq.

Install mmseq 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 mmseq using dnf by running the following command:

sudo dnf -y install mmseq

Install mmseq 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 mmseq using yum by running the following command:

sudo yum -y install mmseq

How To Uninstall mmseq on Fedora 34

To uninstall only the mmseq package we can use the following command:

sudo dnf remove mmseq

mmseq Package Contents on Fedora 34

/usr/bin/bam2hits
/usr/bin/ensembl_gtf_to_gff.pl
/usr/bin/extract_transcripts
/usr/bin/fastagrep.sh
/usr/bin/filterGTF.rb
/usr/bin/haploref.rb
/usr/bin/hitstools
/usr/bin/mmcollapse
/usr/bin/mmdiff
/usr/bin/mmseq
/usr/bin/mouse_strain_transcriptome.sh
/usr/bin/offsetGTF
/usr/bin/t2g_hits
/usr/bin/testregexp.rb
/usr/bin/usage.sh
/usr/lib/.build-id
/usr/lib/.build-id/06
/usr/lib/.build-id/06/6856f3b5023a19bbb532184f9f65d4bc13ca79
/usr/lib/.build-id/0a
/usr/lib/.build-id/0a/de0bd34b51aff375323d72f6d14f5045d2774d
/usr/lib/.build-id/49
/usr/lib/.build-id/49/0570aa6aefe489607f03aa2affee039e008dee
/usr/lib/.build-id/96
/usr/lib/.build-id/96/ff95baaab26f3f1d43ebac1cbe61007d4439e8
/usr/lib/.build-id/99
/usr/lib/.build-id/99/f1b0fd947e04a0734ad00cd6f02cef653a85cd
/usr/lib/.build-id/aa
/usr/lib/.build-id/aa/b6cf1ebdd7784b8c83702efc80dd2b2a0e33e2
/usr/lib/.build-id/d9
/usr/lib/.build-id/d9/9aa6bc3f2341830d1966af06636b8a336e460e
/usr/lib/.build-id/f5
/usr/lib/.build-id/f5/a0a98a44a7183f37d551392e9ab65ebef6c8ff
/usr/share/doc/mmseq
/usr/share/doc/mmseq/COPYING
/usr/share/doc/mmseq/README.md
/usr/share/doc/mmseq/doc
/usr/share/doc/mmseq/doc/332.mat
/usr/share/doc/mmseq/doc/countsDE.md
/usr/share/doc/mmseq/doc/dod2.mat
/usr/share/doc/mmseq/doc/mmdiff-model.png
/usr/share/doc/mmseq/doc/mmseq-collage.png

References

Summary

In this tutorial we learn how to install mmseq on Fedora 34 using yum and dnf.