Available files

This application is written in java, and as such is platform independant. However, it relies on Primer3 and BlastN, which are not. The different platform-dependant packages of PCRTiler differ solely on the platform of the bundled Primer3 and Blast executables. See the system requirements below for further information.

What are the differences between those versions? Which one do I need?

The standalone version has a graphical user interface and provides the same functionality as the server version, while using the resources of the client computer. This is the preferred and easiest option for most users who want to run PCRTiler locally.

The server version is exactly like the one hosted on this web site, and requires a dedicated server and some technical expertise to set up. It uses the resources of the server it is hosted on.

System requirements

Hardware requirements

The server and standalone versions essentially have the same system requirements. The main limiting factor is memory. In our experience, for acceptable performance you need enough memory for the BLAST database (~800Mb for Homo sapiens, ~4Mb for bacteria), plus a maximum of 1Gb for PCRTiler. Therefore, 2Gb of memory should be enough. As for CPU speed, PCRTiler is a multi-threaded application, so it will make use of all available CPU cores: the more you have, the faster it will run.

Software requirements

PCRTiler requires the Java Runtime Environment and, for the server version only, Tomcat 6. To date, it has been shown to work correctly on Linux i386, Windows Vista, Windows XP and Mac OSX.

Installation instructions - standalone

  1. Make sure you have the latest Java Runtime Environment on your computer. This is required for all java applications;
  2. Extract the downloaded PCRTiler package available above in any directory on your computer. PCRTiler will run from your Desktop, for example. If you do not already have a tool to decompress it, you can use WinRar or WinZip.
  3. Open the decompressed folder, and double-click on start.bat on Windows or start.sh on Linux or Mac OSX. The PCRTiler application window should open (screenshot);
  4. PCRTiler requires genome sequences to verify the specificity of oligos. You must download at least one genome if you intend to do specificity checks. Click on the "Configuration" menu, and select "Genome Management" (screenshot);
  5. Click "Sync with Genbank". This will contact Genbank to obtain the latest genome names;
  6. Select the genome you want to do specificity checks against. Click "Download". Once the download is complete, close this dialog box;
  7. The interface should be familiar, since it is identical to the web server version: it is ready to use.

Installation instructions - server

The folowing instructions assume that you have superuser priviledges on the server. All the following commands must be run as root.

  1. Make sure that your system has Java 1.6 and Tomcat 6 installed and running. Installing those is beyond the scope of this document. Please follow their installation instructions. Earlier versions might work too, but have not been tested and therefore are unsupported.
  2. Make sure Tomcat can allocate enough memory. Modify the file /etc/tomcat6/tomcat.conf to specify a higher maximum memory (JAVA_OPTS="-Xmx2000m");
  3. Download and extract the PCRTiler server package to a temporary location:
    cd;
    wget http://pcrtiler.alaingervais.org:8080/PCRTiler/PCRTiler-v1.42-server-linux-i386.tgz;
    tar -xvzf PCRTiler-v1.42-server-linux-i386.tgz;
  4. Execute the install script:
    cd PCRTiler-v1.42;
    ./install.sh
    WARNING: This will delete everything in /var/lib/tomcat6/webapps/PCRTiler and /var/cache/tomcat6/work/PCRTiler. Those are the only directories modified by the script.
  5. Edit the configuration file at /var/cache/tomcat6/work/PCRTiler/config.txt to fit your needs;
  6. Access the PCRTiler web site at http://localhost:8080/PCRTiler
  7. Once you have installed your required genomes, don't forget to disable genome management in /var/cache/tomcat6/work/PCRTiler/config.txt

Please note that the server version was developped under linux. If you can get Tomcat running on Windows XP, there is no reason why PCRTiler-server should not work on those architectures if you install the appropriate binaries of Primer3 and BLAST. However this was not tested and therefore is not officially supported.