You may also find other compiled binaries at time of writing, a second binary called bwamem-lite is also included. You should find it within the same folder ( bwa-0.7.12 in this example). Move to this directory and compile using: cd bwa-0.7.12 This will produce a directory called bwa-0.7.12 containing the files necessary to compile the BWA binary.
Unpack the tar file using: tar xvzf bwa-0.7.12.tar.bz2 Read the overview of the BWA software on the BWA project homepage, then download the latest version of the software package. If so, please adapt the number accordingly in the commands. Note that the version numbers of packages you download may be different than shown in the instructions below. RStudio IDE and R libraries ggplot2 and gsalib.To find out how to do so, you should seek help from your systems administrator. The simplest solution is to install an additional JRE and specify which you want to use at the command-line. If you have a version that does not match the requirements stated above for the version of GATK you are running, the GATK may not run correctly or at all. This should return a message along the lines of ”java version 1.8.0_25” as well as some details on the Runtime Environment (JRE) and Virtual Machine (VM). To test your Java version, run the following command in the shell: java -version All Linux/Unix and MacOS X systems should have a JRE pre-installed, but the version may vary.
Previous versions down to 2.6 required JRE 1.7, and earlier versions required 1.6. Starting with version 3.6, the GATK requires Java Runtime Environment version 1.8 (Java 8). The XCode tools are free but an AppleID may be required to download them. On MacOS X, you may need to install the MacOS Xcode tools. See for relevant information and software downloads. These tools are usually pre-installed on Linux/Unix systems. You will also need to have access to an ANSI compliant C++ compiler and the tools needed for normal compilations (make, shell, the standard library, tar, gunzip).
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