The MEME Suite makes heavy use of Perl, using it for stand-alone tools and webservice wrappers.

Most UNIX-like systems will already have a modern version of Perl but if that is not the case you can get Perl from www.perl.org. If you are working on a system where you don't have administrative rights to install Perl the normal way, or you need to manage multiple versions of Perl then you could also use perlbrew.

Once Perl is installed run the script dependencies.pl in the scripts directory of the MEME Suite installation files.

This will check for the existence of the required and optional Perl modules directly used by the MEME Suite. If it can't find a module it will display a warning giving the module name and a description of the tasks that require it. For example the output might look like this:

In this case all the modules required for running the MEME Suite command line tools have already been installed with the minor exception of Math::CDF which is only needed for a script which probably won't be used anyway.

To install any missing modules simply run Perl's cpan program with the name of the module following. If this is a system installation of Perl you will also need to use sudo.

TROUBLESHOOTING: On Linux, the Perl modules related to XML parsing may also require a system library installed. The Debian package required is called libexpat1-dev so on Ubuntu and related distributions the install command is:

The MEME Suite uses Python for a few tools and scripts like DREME and fasta-dinucleotide-shuffle. Two versions of Python scripts are provided: one for Python 2.7.3 and one for Python 3.x.

Most UNIX-like system will already have Python installed though it possibly won't be the correct version. If you need to install Python the official source is www.python.org however Pypy available from pypy.org is also compatible with the MEME Suite and may offer a speed boost to long running programs like DREME.

The zlib library (http://www.zlib.net/) is used to handle compressed files.

On Apple computers if MacPorts is installed then the developer required tools can be installed with the command:

On Ubuntu and related distributions it can be installed with the command (Note: that is a "1" not an "l" in in "b1g"):

Ghostscript is used to create PNG (portable network graphic) images from EPS (encapsulated postscript) images. Most of the more recent programs in the MEME Suite have the capability to show images in their HTML output even when no PNG images are available.

Alternatively the MEME Suite can make use of the convert program from the ImageMagick package to convert from EPS to PNG format.

The MEME suite makes use of a number of common utilities. In the case of linux these should already be installed but OS X users should follow these instructions.

The tools that most users need are:

• Bourne compatible shell
• C-shell compatible shell
• GNU compatible make
• a C compiler (GCC and Clang are known to work)

Additionally, installers of the web server will need:

• tar
• gzip/gunzip

and developers will also need:

• autoconf
• automake
• libtool
• wget
• ant

On Apple computers if MacPorts is installed then the developer required tools can be installed with these commands:

Ubuntu and related distributions can use the install commands:

1. Install the Apple software development environment, XCode. XCode is a free download from the Apple App store. If you don't have an App store account it can also be downladed from the Apple developer's web site.
2. Download the command line development tools from within XCode. Under the "XCode" menu choose the "Preference ..." item. You'll be presented with a dialog box with several tabs. Select the "Downloads" tab, and click on the button to download the command line tools.

If you are installing the MEME Suite on an Apple computer, you may want to install the MacPorts software. MacPorts will make it much easier to install many other software packages such as Ghostscript, OpenMPI and Tomcat. You can get MacPorts from https://www.macports.org/install.php. To see if MacPorts can install a package for you, just enter a command like

If you want to run the high-speed, parallel version of MEME you will need one of the following MPI implementations:

• OpenMPI from http://www.open-mpi.org
• MPICH from http://www-unix.mcs.anl.gov/mpi/mpich

If you are installing the MEME Suite on an Apple computer and have installed MacPorts (see above), to install OpenMPI you would simply use the following command and MacPorts would do all the work:

Make sure you then execute the command printed out by the install command, which will look something like:

The MEME Suite includes the code for libxml2, libxslt and the extensions in libexslt however it can detect and use these libraries if they are already installed on your computer and this will speed up the build process.

Be warned that the libxslt library is dependent on features in the libxml2 library, so linking errors will occur if you try to use two incompatible versions. If this occurs simply use the configure flags "--enable-build-libxml2" and "--enable-build-libxslt".

Java is used to compile and run the MEME Suite website and the sequence database updater.

The JDK can be retrieved from the Java downloads website. Linux users can alternatively use the OpenJDK.

Ubuntu and related distributions can use the install command:

Ant is Java's equivalent of a Make and is used to build the Java code used by the website. Additionally Ant is used to create a list of the website files when the developer only bootstrap script is run.

On Apple computers if MacPorts is installed then the developer required tools can be installed with the command:

Ubuntu and related distributions can use the install command:

Apache Tomcat is used because it supports Java servlets and can also act as a normal web server.

The Opal toolkit is used to provide web services for the MEME Suite. You should download and install the latest version of Opal.

TROUBLESHOOTING: At the time of writing Opal 2.5 was newly released and the most visible link was still to the previous version. Do not get Opal 2.4 as it is incompatible.

A MEME Suite web server will work without a Batch Scheduler but if too many jobs are submitted performance will be very poor. To avoid this problem, you can install a MEME Suite web server on a compute cluster, which requires one of following batch schedulers:

• PBS from http://www.openpbs.org
• Grid Engine from http://gridscheduler.sourceforge.net

For example for release you should use the commands:

to expand the tarball and move to the root directory of the distribution.

If there are patches associated with the distribution please see section Getting and installing the patches that explains how to download and install the patches.

The configure script is found in the root directory of the distribution and used to set installation parameters. For a list of all available configuration parameters see section Customizing configuration below. Here we will discuss the most common configuration settings. The general form of the configure command is:

Basic configuration parameters

When invoked without any parameters, only the command-line versions of the MEME Suite tools will be installed and none of the web components. The MEME Suite directories will be created under $HOME. The buttons and hyperlinks in the HTML output of the tools will not work. This is safe because you won't be able to send your data over the internet accidentally but it's not very useful. However, if this is what you want the simplest command is:

MEME Suite tool output files contain buttons that will send your results over the Internet when clicked. This is a very useful and powerful feature of the MEME Suite tools. If you want the buttons and hyperlinks in the HTML output of the tools to access the MEME Suite web server at https://meme-suite.org/meme, the simplest configuration command is:

The installation root directory can be specified using the parameter prefix. For example,

This will install only the command-line versions of the MEME Suite tools and none of the web components. The MEME Suite directories will be created under the directory specified by the prefix option. The buttons and hyperlinks in the HTML output of the tools will link to the MEME Suite web server at https://meme-suite.org/meme. This is probably the most common use of configure.

The MEME Suite depends on the libraries libxml2 and libxslt. If these libraries are already installed, MEME will use try to use the installed versions. Otherwise, MEME will build its own copies of these libraries. If for some reason you want to force MEME Suite to build its own copies of libxml2 and libxslt, you can do so by using the --enable-build-libxml2 and --enable-build-libxslt options. For example,

This will cause the MEME Suite to build its own copies of libxml2 and xslt.

Configuring installation of the MEME Suite Web Application

Three parameters are needed to completely configure the MEME Suite web application:

• the URL for the web site hosting the static HTML pages and CGI scripts
• the URL for the web site hosting the MEME Suite SOAP services
• the directory where service configuration files should be put for Opal

In many cases you will be able to take advantage of the default values for these parameters.

The parameter with-url was introduced in the previous section. It sets the URL for the web site hosting the static HTML pages and CGI scripts. If you are installing your own MEME Suite web application you will need to set this parameter.

The parameter enable-web turns on installation of the MEME Suite web site. It can also be used to specify the URL for the MEME Suite SOAP services. The default URL for the MEME Suite SOAP services is https://meme-suite.org/meme/opal2/services. For example,

would install the MEME Suite command line tools and the web application under your install path. The web application would use the MEME Suite SOAP services at https://meme-suite.org/meme/opal2/services to process requests.

An explicit value can also be passed for the enable-web parameter. For example, to explicitly specify the value for the MEME Suite SOAP services on the https://meme-suite.org/meme server:

If you wish to build and install your own MEME Suite SOAP services you must have successfully installed and configured Opal.

You must set the environment variable CATALINA_BASE to the path to the root directory of your Tomcat instance. The environment variable CATALINA_HOME must be set to the root of the Tomcat installation directory. This can typically be done by editing the file named .profile in the home directory to add the following lines:

The parameter enable-webservice is used to specify the location of the webservice deploy folder for Opal. The value may be relative to CATALINA_BASE or absolute. If no value is provided then it will point to a folder called deploy in CATALINA_BASE.

For example, to install the web server and build and provide using your own MEME Suite SOAP services:

To build simply type while at the top directory:

You can run tests to make sure the MEME Suite programs are working correctly. The test will check MEME Suite output against known valid output:

If there are errors, the output files from each test will be kept in tests/results/ and can be compared to files in tests/. When a test passes without errors the output files are removed automatically.

To install the software in the directory tree specified by prefix run the command:

To use the MEME Suite on the command-line you should set the environment variable PATH so that your shell can find the newly installed tools. The primary MEME Suite tools, meme, dreme, meme-chip, mast, fimo, etc., will be stored in the bin subdirectory of the installation. Supporting utilities are stored in the directory named libexec/meme-version # (e.g., $HOME/meme/libexec/meme-) subdirectory. The steps to set your PATH will depend on the shell you use.

For the Bash shell you should edit the file called .bash_profile or .profile in your home directory. Add the following line to include the primary MEME Suite tools in your search PATH:

For C shell (aka csh and the similar tcsh) you should edit the file called .cshrc (or .tcshrc, if you use tcsh) in your home directory to add the following line:

Installing MEME command line programs without any web components in /opt/meme. Buttons in the tool outputs will not work.

Installing MEME command line programs without any web components in /opt/meme. Buttons in the tool outputs will submit to the URL: https://meme-suite.org/meme.

Installing MEME command line programs and the website, but not the SOAP services.

Note that while the compiled tools will be installed to /opt/meme the website will be installed to $CATALINA_BASE/webapps in the form of a Java web archive (meme-.war).

The URL for the MEME web site will be http://host/meme and buttons in the program outputs will submit to that URL. This installation will use the MEME SOAP services on https://meme-suite.org/meme/opal2/services.

Installing the full MEME Suite including all the command line programs, the website, and the SOAP services. The website, and SOAP services will all be served by an installation of Tomcat with Opal. This assumes that Opal is configured to deploy services with configuration files in the default location (check opal.deploy.path in opal distribtion/etc/opal.properties ).

Installing the full MEME Suite as in example 4 but setting the database source to a folder where it can be shared among multiple MEME Suite installs. Additionally the URL to the previous version is set and the notices and news URLs are set to a location in the website root where they can be share by multiple installs.

Did you change it recently? Did you upgrade to a new version? Is your operating system supported? Are you using latest versions of tools required?

Check the frequently asked questions. Check the MEME Suite Q&A forum to see if your problem has been reported and there was a solution. Check the release notes for possible bug fixes and other version-dependent changes.

If your problems are related to the prerequisite software installation, your OS, or compiler, check relevant mailing lists, do a Google search or talk to your system administrator.

Often, the problem is a result of the wrong execution of the commands or typos in the commands. Check if you executed the commands in the right order and if they were typed properly. Sometimes the command-line tools will require details you don't need for a web submission like the sequence alphabet so check that you have included them.

If all fails and you still have the problem, go ahead and send an email to meme-suite@uw.edu.

Here is a guiding list of what to put in your email:

• Use a meaningful and specific subject.
• Write clearly and be precise about your problem.
• Attach any files required to recreate the problem if they are small enough to email (≤ 5MB in total).

If you are reporting a problem with the web server you should also tell us:

• The Web browser you are using (eg. Firefox, Chrome, Safari, Opera or Internet Explorer) including the version.
• A link to the page with the problem. This is especially useful for failed web-service jobs as we can then lookup related logs.

If you are reporting a problem with a copy of the MEME Suite you have installed (or are installing) you should also tell us:

• the MEME Suite version,
• the OS version,
• the autoconf version,
• the compiler version,
• the Perl version, and
• the Python version, as well as,
• attach the file config.log which is created by the configure script
• if there are any errors or warnings output during the make stage, attach make.log created by the following commands (assuming bash shell):
  make clean make &> make.log
• if any tests fail in the make test stage, attach test.log created by the following command (assuming bash shell):
  make test &> test.log
• if there are any errors or warnings output during the make install stage, attach install.log created by the following command (assuming bash shell):
  make install &> install.log