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Installing mPrime

mPrime will run on Windows (XP or later), Linux (Ubuntu 12.04 and CentOS 5 have been tested), and Mac OSX (Intel only). Note that both 32-bit and 64-bit versions of the program are available for each platform. The Windows setup program will install the correct version for your computer. For OSX or Linux, download the 32-bit or 64-bit version as appropriate. The main advantage of the 64-bit version is that whole genome indexes may be searched (locally) on computers with 4GB or more of memory. With the 32-bit version (or on computers with less memory), you must do local searches using the set of chromosome indexes. If you're not sure which version to use, download the 32-bit version (and don't try to search whole genome indexes locally). Platform specific instructions are provided below.

For Windows, run the installer and start the program using the shortcut on your desktop or in the Start menu. The OSX version is distributed as a disk image. Open the disk image, copy the mPrime folder to your home directory and double-click the mPrime icon within that folder. On Linux, untar the mprime3-arch.tar.gz file within your home directory and start the program from a terminal window by changing to the mprime3 directory and entering ./mprime.

Several other programs are also required for mPrime to function; these programs are either part of the mPrime installation package or are routinely part of the operating system installation. These other software requirements include:

Qt toolkit: The user interface uses the Qt toolkit. For Windows and OSX, the appropriate shared libraries are installed in the Qt folder within the installation directory. Because of the way OSX handles shared libraries, you will have a conflict if you have already installed Qt to the /Library/Frameworks directory (not a common occurrence outside of the developer community). To test for that conflict, open a terminal window, change directories to the mPrime 3.0/bin folder, and enter ./mprime. If you have duplicate libraries, you will see a string of error messages indicating that fact in the terminal window. Simply rename the Qt folder in the installation directory to Qt.0 to resolve the problem.

For Linux, you will need to insure that the Qt4 libraries are installed on your system. Try running the mPrime program. If you get an error indicating that the Qt libraries are not installed, you will need to install libqt4-core and libqt4-gui.

primer3: The primer3_core executable must be present in the bin subdirectory of the mPrime folder. The primer3_config folder in the bin directory contains the thermodynamic parameters required by primer3 for computing Tm values. Only version 2 of primer3 is supported by mPrime. The most recent version of the software is primer3-2.3.5, and is available from the primer3 website (http://primer3.sourceforge.net/releases.php). Note that you may need to click on the link to the "SourceForge Downloads Page" to get access to version 2. This version is currently available only as source code, so to update to a newer version of the primer3 program, you may need to compile it yourself. The compiled primer3 executable from the version dated 5/3/2012 is included in the mPrime package.

Bowtie: The Bowtie software package for various platforms is available from http://bowtie-bio.sourceforge.net. The mPrime package includes the required bowtie and bowtie-build executables from version 1.0.0, which is installed in the bin subdirectory of the mPrime folder. You will also need a set of Bowtie index files for your desired genome. A set of files for the mouse, human, and rat genomes, with each chromosome in a separate index, is available from the mPrime website. Whole genome and cDNA indexes for these three species are also available from the mPrime website, or you could make your own following directions in the Bowtie manual.

curl: The curl program is required to download sequence data from the Ensembl DAS Reference Servers. It is installed in the bin subdirectory of the mPrime folder on Windows, but is generally already present on OSX systems. On Linux the wget program is used instead. To check for the presence of wget (or curl) on these systems, open a terminal window and enter "wget" (or "curl"); if you get an error message indicating that the program is not found, install it to your system.

zlib: The zlib library is required to allow reading of compressed sequence files. If this library is not present, you will get an error the first time you attempt to load a fasta file (compressed or not). The zlib1.dll file (version 1.2.7) is installed in the bin subdirectory of the mPrime package on Windows. This library is generally present on OSX or Linux systems. For OSX, make sure that the file libz.dylib is present in the /usr/lib directory. On Linux, insure that libz.so.1 is in /usr/lib. On some systems you may need to make a symbolic link with the above name to the installed version of libz.

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