installation - njdbickhart/RAPTR-SV GitHub Wiki

#Installation

RAPTR-SV has several Java libraries packaged into the main jar executable that is distributed in the "releases" of this github page, but there are still some external dependencies that you need to provide at this time.

##Setting up the proper java runtime environment First, you will need to install java version 1.8 in order to get the most out of RAPTR-SV. If you are using a server that has multiple users currently working simultaneously on it, your best bet on installing java 1.8 is to contact your server's admin and ask him/her to install it for you. If that doesn't work (or the server admin is especially irritable that you would even THINK to ask him/her to do this), then you can perform a manual installation of java by downloading the Java SE package from Oracle's website.

If you are downloading the RAPTR-SV release packages, you may have noticed that there was an executable file within each release titled: "RAPTR-SV.jar." The file extension (".jar") indicates that this is a java archive file. In order to run this using the java executable, you just invoke it on the command line like so:

$ path/to/exe/java -jar RAPTR-SV.jar

or with the following command, if java 1.8 is on your PATH:

$ java -jar RAPTR-SV.jar

If your java installation is correct (and you're running java 1.8) you should get a message on the console from RAPTR-SV, giving the version of the software as well as a "help menu." In order to test that you have the right version of java, type the following into the command line:

$ java --version

##Downloading and installing MrsFAST RAPTR-SV uses MrsFAST to realign split read fragments to the reference genome that you provide. If you do not have MrsFAST on your PATH, RAPTR-SV preprocess mode will exit prematurely without analyzing your data to completion. In order to install MrsFAST, you should first try the system administrator trick mentioned above in the java installation section. If that fails, you can download the source code from the MrsFAST sourceforge page. Please note that you will have to download the source code using "git" in order to proceed. To do this, type the following command into your terminal (preferably in your "home" folder):

$ git clone git://git.code.sf.net/p/mrsfast/code mrsfast 

After you download MrsFAST, you will need to compile the source code into a binary executable. Thankfully, the authors of the program have included a Makefile that does all of this for you! To compile, just cd to the mrsfast directory and run "make." An example below:

$ cd home/user/mrsfast-ultra-directory
$ make

Unlike the Java executable, MrsFAST is called from RAPTR-SV natively, so MrsFAST needs to be on your PATH. An easy way to do this is to copy the executable to your "bin" folder within your home directory using cp.

$ cp mrsfast-ultra-directory/mrsfast ~/bin/mrsfast

To check whether or not MrsFAST is on your path, type the following command:

$ which mrsfast

If the command returns a directory (and not an error message), then MrsFAST is properly installed.