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GATK is supported on all flavors of reasonably recent Linux/Unix and MacOS X systems, but NOT on Windows. The analyses we run in workshops are designed to run quickly and on small datasets, so should not require more than 2G of RAM. For file storage, plan on 10G of space (but I would be shocked if we get to half of that).
Mac Shell Shocked Download Zip
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The current version of GATK requires Java Runtime Environment version 1.8. All Linux/Unix and MacOS X systems should have a JRE pre-installed, but the version may vary. To test your Java version, run the following command in the shell:
Read the overview of the Picard software on the Picard project homepage, then download the latest version (currently 2.4.1) of the package containing the pre-compiled program file (the picard-tools-2.x.y.zip file).
However, you can set up a shortcut called an "environment variable" in your shell profile configuration to make this easier. The idea is that you create a variable that tells your system where to find a given jar, like this:
The exact way to set this up depends on what shell you're using and how your environment is configured. We like this overview and tutorial which explains how it all works; but if you are new to the command line environment and you find this too much too deal with, we recommend asking for help from your institution's IT support group.
In order to access the downloads, you need to register for a free account on the GATK support forum. You will also need to read and accept the license agreement before downloading the GATK software package. Note that if you intend to use the GATK for commercial purposes, you will need to purchase a license. See the licensing page for an overview of the commercial licensing conditions.
The Integrated Genomics Viewer is a genome browser that allows you to view BAM, VCF and other genomic file information in context. It has a graphical user interface that is very easy to use, and can be downloaded for free (though registration is required) from this website. We encourage you to read through IGV's very helpful user guide, which includes many detailed tutorials that will help you use the program most effectively.
This will download and install the ggplot2 library as well as any other library packages that ggplot2 depends on for its operation. Note that some users have reported having to install two additional package themselves, called reshape and gplots, which you can do as follows:
After unzipping the file, follow the instructions in the README file that's included in the download package. On a Mac, moving the package to your preferred location and adding the rtg binary to your path to make it available on the command line is sufficient to complete the installation process.
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