How To Install stops on Fedora 34
In this tutorial, we will discuss How To Install stops on Fedora 34
yum package managers.
Also, we will demonstrate how to uninstall and update
stops as well.
If you are only interested in the installation command, here is a quick answer for you:
or if you use
sudo yum makecache && sudo yum -y install staden
sudo dnf makecache && sudo dnf -y install staden
But if you are interested in the details with step-by-step instructions, the following information will be helpful.
Short description: DNA sequence assembly (Gap4/Gap5), editing and analysis tools
First things first, you will need access to a server or computer running Fedora 34. This guide was written specifically with a server running Fedora 34 in mind, although it should also work on older, supported versions of the operating system.
Also, make sure you are running a regular, non-root user with sudo privileges configured on your server. When you have an account available, log in as your non-root user to begin.
There are several ways to install stops on Fedora 34. You can use (links are clickable):
In the following sections, we will describe each method in detail. You can choose one of them or refer to the recommended one.
First, update dnf packages database with
dnf by running the next command:
sudo dnf makecache --refresh
After updating database,
You can install stops using
dnf by running the
sudo dnf -y install staden
Because stops is available in Fedora 34’s default
it is possible to install it from these repositories using the
To begin, update local packages database with
yum using the following command.
sudo yum makecache --refresh
Now can install stops package on your server/computer by running the following command:
sudo yum -y install staden
To update all the packages available on the system:
If you want to update a specific package like stops in this example you should use the following command:
yum update staden
To downgrade a package to an earlier version:
yum downgrade staden
When you run the
dnf update, all system packages with available updates are updated.
However, if you want to upgrade a single package, then you would have to pass the package name as
the argument to the dnf update command.
dnf update staden
To uninstall only the
stops package you can execute
sudo dnf remove staden
Staden is a fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin). Gap4 performs sequence assembly, contig ordering based on read pair data, contig joining based on sequence comparisons, assembly checking, repeat searching, experiment suggestion, read pair analysis and contig editing. It has graphical views of contigs, templates, readings and traces which all scroll in register. Contig editor searches and experiment suggestion routines use confidence values to calculate the confidence of the consensus sequence and hence identify only places requiring visual trace inspection or extra data. The result is extremely rapid finishing and a consensus of known accuracy. Pregap4 provides a graphical user interface to set up the processing required to prepare trace data for assembly or analysis, and automates these processes. Trev is a rapid and flexible viewer and editor for ABI, ALF, SCF and ZTR trace files. Prefinish analyses partially completed sequence assemblies and suggests the most efficient set of experiments to help finish the project. Tracediff and hetscan automatically locate mutations by comparing trace data against reference traces. They annotate the mutations found ready for viewing in gap4. Spin analyses nucleotide sequences to find genes, restriction sites, motifs, etc. It can perform translations, find open reading frames, count codons, etc. Many results are presented graphically and a sliding sequence window is linked to the graphics cursor. Spin also compares pairs of sequences in many ways. It has very rapid dot matrix analysis, global and local alignment algorithms, plus a sliding sequence window linked to the graphical plots. It can compare nucleic acid against nucleic acid, protein against protein, and protein against nucleic acid.
You now have a full guide on how to install
yum package managers.
Also, we showed how to update manually as a single package and different ways to uninstall
the stops from Fedora 34.