#SAMTOOLS MACOS HOMEBREW HOW TO#
#SAMTOOLS MACOS HOMEBREW INSTALL#
#SAMTOOLS MACOS HOMEBREW FULL#
#SAMTOOLS MACOS HOMEBREW SOFTWARE#

arguments such as input files or parameters) used by the program to perform that command. This means you first make the call to the binary ( samtools), then you specify which command (method) you wish to use (e.g. As the Usage line states, to use SAMtools you will always build your command lines like this: This should print out some version information as well as a list of commands. Finally, add the SAMtools binary to your path to make it available on the command line. You should find it within the same folder ( samtools-0.1.2 in this example). Move to this directory and compile using: This will produce a directory called samtools-0.1.2 containing the files necessary to compile the SAMtools binary.

#SAMTOOLS MACOS HOMEBREW SOFTWARE#

Read the overview of the SAMtools software on the SAMtools project homepage, then download the latest version of the software package. This means you first make the call to the binary ( bwa), then you specify which command (method) you wish to use (e.g. As the Usage line states, to use BWA you will always build your command lines like this:

This should print out some version and author information as well as a list of commands. Finally, just add the BWA binary to your path to make it available on the command line. You may also find other compiled binaries at the 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). This will produce a directory called bwa-0.7.12 containing the files necessary to compile the BWA binary. 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.

#SAMTOOLS MACOS HOMEBREW HOW TO#

To find out how to do so, you should seek help from your systems administrator.

#SAMTOOLS MACOS HOMEBREW INSTALL#

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: 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. See Apple's Xcode site for relevant information and software downloads. On MacOS X, you may need to install the MacOS Xcode tools. 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). Command-line shell, terminal or console.There are also many good online tutorials you can use to learn the necessary notions. If you are unfamiliar with any of the following, you should consult a more experienced colleague or your systems administrator if you have one. To follow these instructions, you will need to have a basic understanding of the meaning of the following words and command-line operations.

#SAMTOOLS MACOS HOMEBREW FULL#

Full in-depth and up-to-date information is available here. Install all software packages required to follow the GATK Best Practices.

Samtools macos homebrew