• Install Tar Mac
• Install Tar Windows
• Install Software From Tar Mac Download
• Mac Tar File

Introduction

While working in Linux, you may have seen downloadable files with the .rpm extension. Rpm files are designed to be downloaded and installed independently, outside of a software repository.

• Jun 25, 2009  The options we gave tar are as follows:-z to tell tar to run this file through gzip to decompress (use -j for bzip files)-x to extract the files-v for “verbose”, so we can see a list of the files it’s extracting-f to tell tar that we’re working with a file; For easier unzipping, see the Tips section at the bottom of this page.
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This guide will show you how to install a .rpm file to your Linux CentOS or Fedora system.

RPM Package Manager (RPM) is a free and open-source package management system for installing, uninstalling and managing software packages in Linux.

Prerequisites

• A user account with sudo privileges
• Access to a terminal window / command line (Menu > applications > utilities > terminal, Ctrl-Alt-F2)
• RPM, DNF, & YUM Package Managers (all included by default)

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Typically, a web browser is used to locate and download a .rpm file. However, if a browser is not available you can still download a file if you know where it’s located.

You may need to install a software tool called wget.

To install wget in CentOS, enter the following in a terminal window:

To install weget in Fedora, enter the following:

Now, you can use the wget command to download the .rpm file you want. Enter the following:

The system should reach out to the website and download the file to your current working directory.

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Note: You can look up the address of a particular .rpm file in a web browser on another system. Also, this is a handy way to install more recent software versions or special non-standard software. Also, take care when installing software packages! Make sure you trust the source before you install. Usually, a developer will include a verification method to make sure you're getting authentic software.

Step 2: Install RPM File on Linux

To install a .rpm package in CentOS Linux, enter the following:

The –i switch tells the package manager you want to install the file.

More information on the RPM installer can be found in the RPM documentation.

Alternately, you can use the yum package manager to install .rpm files.

Enter the following:

The localinstall option instructions yum to look at your current working directory for the installation file.

Note: YUM stands for Yellowdog Updater Modified. Normally, yum looks to your enabled software repositories for new software packages to install. More recent verbiage suggests using install instead of localinstall, but it's up to you.

To install an .rpm package on Fedora Linux, enter the following:

Just as in CentOS, the –i switch tells RPM to install the software.

Another method is to use the dnf utility to install the package:

Unlike many Linux tools, DNF is not a set of initials. It is merely the next evolution of the yum package manager.

The RPM installer can be used to remove (or uninstall) a software package.

Enter the following into a terminal window:

The –e option instructs RPM to erase the software.

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To check the .rpm file for dependencies using the following command:

The system should list all the dependencies:

• –q – This option tells RPM to query the file
• –p – This option lets you specify the target package to query
• –R – This lists the requirements for the package

If there are any missing dependencies, you can install them from the standard repositories using yum or dnf. If your software requires other non-standard software, it will often be noted in the installation instructions.

One exciting feature of the yum package manager is that it allows you to download .rpm files directly from the repository. This might be helpful if you have limited bandwidth, or want to copy a single downloaded file between systems. It could also help if you have intermittent internet access, and you don’t want to spend time waiting for your installer to finish.

To download a .rpm file from the repositories, enter the following:

If you wanted to download the files for Apache, for instance, you’d replace packagename with httpd. You can then install the file as above.

Note: In Linux, administrators find it helpful to have a single tool to manage software. That tool – called a package manager – can install software, keep track of software requirements, and track updates and patches. Package managers also work with repositories, which are secure and standardized libraries of commonly-used and well-supported applications. If you had to install wget in Step 1, that's an example of installing from a repository.

Conclusion

In this tutorial, we covered three different options for installing RPM files on Linux.

As with most Linux software, your default package manager makes it simple to track installations, updates, and prerequisites.

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Downloading and installing the SRA Toolkit

• If you are using a web browser, the following page contains download links to the most current version of the toolkit for each of the supported platforms:
  SRA Toolkit download page: Download Page
• If you are instead working from a command line interface, you may use FTP or wget to obtain the software from the following directory: 'http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current'.
  Example: wget 'http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-centos_linux64.tar.gz'

Unpacking the Toolkit

• Unix:tar -xzf sratoolkit.current-centos_linux64.tar.gz
• Mac OSX: Double-click on the .tar.gz file and the Archive Utility will unpack it. Alternatively, command-line tar will also work (see Linux example, above).
• Windows: use an archiving and compression utility (e.g., Winzip, 7-Zip, etc.), or simply double-click on the .zip file and drag the 'sratoolkit..' folder to the preferred install location.

Note: For most users, the Toolkit functions (fastq-dump, sam-dump, etc.) will not be located in their PATH environmental variable. This may require providing directory information about the location of the Toolkit. See the below examples for how 'fastq-dump' would be called in different circumstances:

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• ~/[user_name]/sra-toolkit/fastq-dump
  The Toolkit 'bin' directory has been placed in the user-specified directory 'sra-toolkit'
• ./fastq-dump
  The Toolkit components are the in the current working directory
• fastq-dump
  If the toolkit location is not specified in your $PATH variable, then the OS cannot locate the fastq-dump program, even if it is in the current directory.
  NOTE: Windows users should be able to enter only 'fastq-dump.exe' if you have navigated to the Toolkit 'bin' directory.

Testing the Toolkit Configuration

The Toolkit comes with a default configuration that will work for most users. You may elect to perform the following tests to confirm that your configuration is working correctly. The default location for the 'download repository' is:

• Linux:/home/[user_name]/ncbi/public
• Mac OSX:/Users/[user_name]/ncbi/public
• Windows:C:Users[user_name]ncbipublic

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Note that if the tests fail, or if you wish to specify the download location for files sourced from NCBI, you should configure your Toolkit installation. During normal operation, the Toolkit may be required to download the following types of data to the default location:

• Reference sequences: Small (most less than 70 MB) sequences used to decompress aligned SRA data.
• SRA data files: If data are downloaded 'on-demand' using the toolkit, then partial and whole SRA datasets (most are several Gb in size) can be located here. Note: Manually downloaded SRA data obtained using a web browser, wget, ascp, or FTP may be stored anywhere in the local file system.

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For the test, we are using an arbitrary dataset, SRR390728 (RNA-Seq (polyA+) analysis of DLBCL cell line HS0798), from the National Cancer Institute’s Cancer Genome Characterization Initiative (CGCI) Project. It is a reasonably small SRA dataset that contains aligned (reference-compressed) data, allowing us to test multiple aspects of the toolkit simultaneously.

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• Open a terminal or command prompt and 'cd' into the directory containing the toolkit executables
  (e.g., [download_location]/sratoolkit[version]/bin/).
  • Linux/Mac OSX:./fastq-dump -X 5 -Z SRR390728
  • Windows:fastq-dump.exe -X 5 -Z SRR390728
• If successful, the test should connect to NCBI, download a small amount of data from SRR390728 and the reference sequence needed to extract the data, and stream the first 5 spots of the file ('-X 5' option) to the screen ('-Z' option).
• If the configuration is not valid, an error like the following will likely be displayed:
  fastq-dump.2.x err: item not found while constructing within virtual database module - the path 'SRR390728' cannot be opened as database or table'
• If you receive an error like the one above, please configure the toolkit (described in the next section). If you have already configured the toolkit but are still unable to complete the test successfully, please email [email protected] with a full description of steps taken and error messages received.