How To Install glimmer on Fedora 34
glimmer is System for finding genes in microbial DNA
Introduction
In this tutorial we learn how to install glimmer on Fedora 34.
What is glimmer
Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA.
We can use yum or dnf to install glimmer on Fedora 34. In this tutorial we discuss both methods but you only need to choose one of method to install glimmer.
Install glimmer 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 glimmer using dnf by running the following command:
sudo dnf -y install glimmer
Install glimmer 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 glimmer using yum by running the following command:
sudo yum -y install glimmer
How To Uninstall glimmer on Fedora 34
To uninstall only the glimmer package we can use the following command:
sudo dnf remove glimmer
glimmer Package Contents on Fedora 34
/usr/bin/g3-from-scratch.csh
/usr/bin/g3-from-training.csh
/usr/bin/g3-iterated.csh
/usr/bin/glimmer3
/usr/lib/.build-id
/usr/lib/.build-id/01
/usr/lib/.build-id/01/06c4f8be1aaa066acb7ba8bfc4d9d7da1ca94b
/usr/lib/.build-id/19
/usr/lib/.build-id/19/3e51af0d08a8d18fc97c4b6d143fd452d7daa8
/usr/lib/.build-id/27
/usr/lib/.build-id/27/97a0830c39c970fe2b84ed0cf229db6c3effaf
/usr/lib/.build-id/5b
/usr/lib/.build-id/5b/d7f5c3cb4af0e9fe6c61d9c43d56a87936cbc5
/usr/lib/.build-id/72
/usr/lib/.build-id/72/0a8093c69da4ae909bc86c8e09c882a34e6298
/usr/lib/.build-id/a7
/usr/lib/.build-id/a7/ee6145d37eade39d15878b01eccb6d3cf90444
/usr/lib/.build-id/a9
/usr/lib/.build-id/a9/a2afa9048585904e218fecf380438207d4f400
/usr/lib/.build-id/b0
/usr/lib/.build-id/b0/38b4701c760da11519c5c040dea703c9e54185
/usr/lib/.build-id/c9
/usr/lib/.build-id/c9/c46b38e58a31c274d06826fd125cb50ccac82a
/usr/lib/.build-id/d0
/usr/lib/.build-id/d0/d803df5a8d7886211d9b2bb9372273e036fbf5
/usr/lib/.build-id/e9
/usr/lib/.build-id/e9/342d8163976eba29f20475ef51a13982482054
/usr/lib/.build-id/ed
/usr/lib/.build-id/ed/4073bc1392d254b8130153f83349c35121efbf
/usr/lib/.build-id/f1
/usr/lib/.build-id/f1/3fdc755c1c7552a8daf874649bc6789f24da43
/usr/libexec/glimmer3
/usr/libexec/glimmer3/anomaly
/usr/libexec/glimmer3/build-fixed
/usr/libexec/glimmer3/build-icm
/usr/libexec/glimmer3/entropy-profile
/usr/libexec/glimmer3/entropy-score
/usr/libexec/glimmer3/extract
/usr/libexec/glimmer3/glimmer3
/usr/libexec/glimmer3/long-orfs
/usr/libexec/glimmer3/multi-extract
/usr/libexec/glimmer3/score-fixed
/usr/libexec/glimmer3/start-codon-distrib
/usr/libexec/glimmer3/uncovered
/usr/libexec/glimmer3/window-acgt
/usr/share/doc/glimmer
/usr/share/doc/glimmer/LICENSE
/usr/share/doc/glimmer/glim302notes.pdf
/usr/share/doc/glimmer/sample-run
/usr/share/doc/glimmer/sample-run/from-scratch.detail
/usr/share/doc/glimmer/sample-run/from-scratch.icm
/usr/share/doc/glimmer/sample-run/from-scratch.longorfs
/usr/share/doc/glimmer/sample-run/from-scratch.predict
/usr/share/doc/glimmer/sample-run/from-scratch.train
/usr/share/doc/glimmer/sample-run/from-training.detail
/usr/share/doc/glimmer/sample-run/from-training.icm
/usr/share/doc/glimmer/sample-run/from-training.motif
/usr/share/doc/glimmer/sample-run/from-training.predict
/usr/share/doc/glimmer/sample-run/from-training.train
/usr/share/doc/glimmer/sample-run/from-training.upstream
/usr/share/doc/glimmer/sample-run/iterated.coords
/usr/share/doc/glimmer/sample-run/iterated.detail
/usr/share/doc/glimmer/sample-run/iterated.icm
/usr/share/doc/glimmer/sample-run/iterated.longorfs
/usr/share/doc/glimmer/sample-run/iterated.motif
/usr/share/doc/glimmer/sample-run/iterated.predict
/usr/share/doc/glimmer/sample-run/iterated.run1.detail
/usr/share/doc/glimmer/sample-run/iterated.run1.predict
/usr/share/doc/glimmer/sample-run/iterated.train
/usr/share/doc/glimmer/sample-run/iterated.upstream
/usr/share/doc/glimmer/sample-run/tpall.fna
/usr/share/doc/glimmer/sample-run/tpall.nh
/usr/share/glimmer3
/usr/share/glimmer3/get-motif-counts.awk
/usr/share/glimmer3/glim-diff.awk
/usr/share/glimmer3/match-list-col.awk
/usr/share/glimmer3/not-acgt.awk
/usr/share/glimmer3/upstream-coords.awk
References
Summary
In this tutorial we learn how to install glimmer on Fedora 34 using yum and dnf.