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The MEME Suite Motif-based sequence analysis tools Installation of the MEME Suite The MEME Suite consists of several command line programs and an optional web server. Building and installing the command line programs is very straight-forward. See the 'Quick Install' link below to get started. Installing the web server requires more detailed configuration information. The MEME Suite web server is implemented using static HTML pages, Java servlets, and services. The SOAP services are provided through and, and you should consult the Tomcat and Opal documentation if you wish to install a MEME Suite webserver.

In addition, the web server requires that a batch scheduler be installed, and SGE and PBS are known to work. Table of Contents:. For mac osx mavericks dl data file converter cyv (1 0. Quick Install (for Linux, OS X and Cygwin systems). Type the following commands.

Export PATH=$HOME/meme/bin:$PATH Notes:. This installs only the command-line versions of programs. Refer to if you wish to install your own MEME Suite Web Application as well. This will overwrite any previously existing $HOME/meme directory you already may have installed. You can set the directory to something different in the configure command using the -prefix option.

The HTML output of programs will contain buttons that send your data to for additional processing when clicked. Refer to the if you do not want this feature. The -enable-build-libxml2 -enable-build-libxslt flags use the bundled versions of libxml2, libxslt and libexslt. You can omit these flags and use the system installed copies but ensure that they are compatible as otherwise linker errors will occur. TROUBLESHOOTING: If you get errors during this install it is probably due to your computer not having the installed.

You will want to read that section of this manual and run the dependencies.pl script as described there to see what you may be missing. 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. 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. Once Perl is installed run the script dependencies.pl in the scripts directory of the MEME Suite installation files. Checking Required Perl Modules: Math::CDF missing.

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Only required for fasta-enriched-center script (which is not called by the web scripts). Checking Optional Modules: 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. 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. 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.

On Apple computers if is installed then the developer required tools can be installed with these commands. The MEME Suite includes the code for, and the extensions in however it can detect and use these libaries 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 Development Kit Standard Edition (version 6 or higher) for web server or developer only.

Releases of the MEME Suite are available from (the link opens in a inline frame to provide navigation). The releases are listed with the most recent at the top. For each release we make avaliable:. a README file describing the release and patches,. a pre-patched distribution so you don't have to apply the patches,. the original distribution, and. all of the released patches.

We recommend downloading the pre-patched distribution as it makes the installation process easier but if for some reason you want to use the original distribution and apply patches to it please refer to the distribution specific readme. Getting and installing the patches. The distribution may have one or more patches associated with it. Where possible we recommend you use the pre-patched version as it is often easier, however if you wish to install the patches they are available from (the link opens in a inline frame to provide navigation). With each release there will be a readme and this file will link to any patches and give instructions on the correct installation process. Patches must be installed in release order because a later patch may rely on changes made by an earlier patch. The most common series of commands needed to install a patch are as follows.

Installation of MEME Suite will create the following directories: bin/ db/ doc/ etc/ lib/ LOGS/ The directories contain: bin/ MEME Suite executables and scripts db/ this directory or DIR specified by -with-db=DIR option is created. This directory should contain a folder motifdatabases which contains the motif databases, a folder gomodatabases which contains the gomo databases and a folder fastadatabases which contains the sequence databases. Doc/ Documentation for the MEME Suite tools. This directory is included in the web archive when the web site is installed. Etc/ contains the following files. prior1.plib, prior30.plib - these files are used by MEME.xsl - XML style sheets for creating HTML output from XML for some MEME Suite tools.html,.js,.css - templates used for creating HTML output for some MEME Suite tools.eps - templates used for creating images for some MEME Suite tools. Lib/ contains Perl modules and Python libraries that are included with the MEME Suite.

LOGS/ directory for temporary files created by webservice scripts when jobs are submitted via the website. When installing the website the MEME Suite will put the web archive meme.war in the directory $CATALINAHOME/webapps and the SQLite library sqlite-jdbc-x.x.x.jar in the directory $CATALINAHOME/lib. Installing from a tarball. If you're setting up a web accessable install it is recommended to create a meme user prior to installation.

Put the tarball you obtained from the web site in a directory where you want to build the software. If the software distribution was obtained via Mercurial access please see section. Four steps are required to install the MEME Suite from a distribution tarball:. Unzip and untar the distribution.

Configure the installation using the configure command. Build MEME Suite using the make command. Test the MEME Suite build by using the make test command. Install MEME Suite using the make install command. Unzip and untar the distribution./configure -prefix= $HOME/meme your install path -with-url='This will install only the command-line versions of the MEME Suite tools and none of the web components.

The 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. This is probably the most common use of configure. The MEME Suite depends on the libraries. 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 and, you can do so by using the enable-build-libxml2 and enable-build-libxslt parameters./configure -prefix= $HOME/meme your install path -enable-build-libxml2 -enable-build-libxslt This will cause the MEME Suite to build its own copies of. 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. The process of configuring, building, and installing MEME Suite from a Mercurial repository is the same as, but with two extra, initial steps: you must check out the repository, and you must run the bootstrap script.

Access to the Mercurial repository is granted at this point only to the MEME developers. We provide the tarball distribution of the latest version on the ftp site. If you have Mercurial access and have added your public key to your bitbucket profile, you can check out the source code with the command. By default, configure will establish if your system has the right software to produce parallel version of MEME. Parallel compilation is disabled if MPI is not found or if you specify the -enable-serial option. To compile the parallel version of MEME, 'configure' looks for mpicc, openmpicc or mpcc.

For running the parallel version of MEME, configure' looks on your PATH for MPI programs mpirun or openmpirun. If your MPI is installed in non-standard place, use -with-mpidir= MPI directory option when running 'configure' to specify the MPI installation directory. The parallel version of MEME is compiled and installed automatically via commands make and make install. Please see section for information where to get the MPI software. Currently, the parallel version of MEME is known to work with: MPI distributions MPICH OpenMPI MEME also works with some versions of LAM MPI, but LAM has been superceded by OpenMPI, and is no longer under active development. Customizing configuration. Customization is done via the command line arguments to configure.

The general syntax for all the options is one of the following:. Include a feature: -enable-feature or -enable-feature=yes. Do not include a feature: -disable-feature or -enable-feature=no.

Set a specific feature to a value: -with-feature= value or -enable-feature = optional value. Text in a dashed rectangle is optional: optional text The following table provides a list of parameters available for configure: Option Needed for Default value -prefix=​ install path Provide the installation location path. $HOME -enable-build-libxml2 Forces MEME Suite to build and use libxml2 code included in MEME Suite distribution. Disabled -enable-build-libxslt Forces MEME Suite to build and use libxslt code included in MEME Suite distribution.

Disabled -enable-debug Produce an executable with debugging symbols. No debug -enable-opt Produce an executable with optimization. Compiler and OS dependent.enable-serial Produce only serial version of MEME, do not build parallel version.

Disabled -enable-web =​ opal services url Build web site applications. Must point it to MEME Suite web services exposed via Opal.

Defaults to when the URL is not provided. Disabled -enable-webservice =​ opal deploy folder Deploy MEME Suite web services utilizing an existing Opal installation. The path to the deploy folder can be relative to CATALINAHOME or absolute. If it is not specified than it is set to the folder deploy in CATALINAHOME. Disabled -with-contact=​ site administrator email Set email of web site administrator. No site contact.with-dev-contact=​ developers email Set email of developers.

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Meme-suite@uw.edu -with-convert=​ path to convert binary Set location of ImageMagick convert application. This is only used if Ghostscript can not be used.

See also '-with-gs'. As found in PATH -with-db=​ database directory Set path to databases. Install path /db/ -with-gs=​ path to gs binary Set location of Ghostscript application. As found in PATH -with-logs=​ logs directory Set path to logs. Install path /LOGS/ -with-maxtime=​ max job time Set wall time limit (sec) a web-submitted job started by the web server may use.

18000 (5 hours) -with-mpidir=​ mpi directory Set MPI installation path. Path of found mpicc -with-perl=​ path to perl binary Set location of Perl interpreter. As found in PATH -with-python=​ path to python binary Set location of Python interpreter. As found in PATH -with-url=​ url Set URL for the MEME Suite web site used by buttons on the output of MEME Suite tools. No URL is used.with-prev-url=​ url Set URL pointing to a install of the previous release. This will create a link in the menu allowing users to easily navigate to the previous release.

The option -with-prev-ver must also be provided. No link is created.with-prev-ver=​ version number Set the version number of the previous release. This will create a link in the menu allowing users to easily navigate to the previous release.

The option -with-prev-url must also be provided. No link is created.with-goserver-url=​ url Set URL for the GO term details page. The identifier will be substituted for GOTERMID.with-quota=​ COUNT/TIME Set the quota limit for job submissions through the website as a COUNT of submissions during TIME seconds. No quota limits.with-notices=​ notices file name Sets the URL of the notices file relative to the top directory of the webapp.

Notices file name The notices file is intended to contain important information and is displayed to users when they visit the MEME Suite site. The user can click a button to hide the notices until the next session or until the notices file is updated.

The default location for the notices file is in the top directory of the installation, but any file placed there will be deleted if the MEME Suite is reinstalled. To prevent this, you can instead place it in another servable directory (e.g, webapps/messages) and specify./messages/notices.txt as the notices file name. If you have more than one version of MEME Suite installed, you can specify a different notices file for each one (e.g.,./messages/notices.txt). The notices file is written in the dialect of known as. The notices file is expected to be called notices.txt and is in the top directory of the webapp.

News file name The news file is intended to contain non-essential news and is displayed to users when they visit the MEME Suite site and there are no notices to display. The user can click a button to hide the news until it is updated. The default location for the news file is in the top directory of the installation, but any file placed there will be deleted if the MEME Suite is reinstalled. To prevent this, you can instead place it in another servable directory (e.g, webapps/messages) and specify./messages/news.txt as the news file name. If you have more than one version of MEME Suite installed, you can specify a different news file for each one (e.g.,./messages/news.txt). The news file is written in the dialect of known as.

The news file is expected to be called news.txt and is in the top directory of the webapp. Update-sequence-db your install path/db/fastadatabases The above command will cause databases to be downloaded from all the default sources. If you are installing multiple versions of the MEME Suite then you will probably want to use a single set of sequence databases. By using the configure option ‑‑with‑db= path to databases you can point multiple MEME installs at the same folder. Note: there is a known bug with some older versions of the MEME Suite where the -with-db configure option does not work, in these cases we suggest removing the your install path/db folder and replacing it with a symlink to your preferred location after installation.

Additionally to be backwards compatible with releases older than 4.10.0 you will need to generate a CSV index listing the downloaded databases. This can be achieved with the -csv option.

Update-sequence-db -csv path to databases/fastadatabases cp path to databases/fastadatabases/fastadb.csv path to old distribution/etc/ cp path to databases/fastadatabases/fastadb.index path to old install/etc/ After the csv and index files are generated you need to move the index files to the etc folders of all your. Update-sequence-db -norsat path to databases/fastadatabases This command will download from all the available sources except the upstream sequences from Regulatory Sequences Analysis Tools.

It can take a long time to completely download all the sequences but you can stop the process at any point by pressing enter to switch the program to command mode and then typing the command 'exit' and pressing enter again. In order to keep the sequence databases current, you can place one of the above commands in a chron job that runs at regular intervals. After updating the databases you should restart the all the MEME Suite web applications. Installing motif databases Tomtom, MEME-ChIP, SpaMo, CentriMo and AME can make use of motif databases. Mv motifdatabases path to databases/motifdatabases Where the path to databases may just be the db folder in the installation or another location if the ‑‑with‑db= path to databases configure option was specified.

On a split install you should install the motif databases on both servers. Note: releases prior to 4.10.0 also require the motifdb.csv file to be copied into the distribution's etc directory and the rerunning of make install to generate and install the motifdb.index file. After updating the databases you should restart the all the MEME Suite web applications. Installing GOMO databases. Mv gomodatabases path to databases/gomodatabases Where the path to databases may just be the db folder in the installation or another location if the ‑‑with‑db= path to databases configure option was specified.

On a split install this only needs to be done on the services install. In a split install copy the file gomodatabases/gomodb.csv to the etc folder of the website install.

Note: releases prior to 4.10.0 require copying the gomodb.csv file into the distribution's etc directory and rerunning make install to generate and install the gomodb.index file. After updating the databases you should restart the all the MEME Suite web applications. Reporting problems. If all fails and you still have the problem, go ahead and send an email to. That email address is monitored by about 4 of us, and we're based in both Australia and the USA so we can generally answer your queries more quickly than if you emailed us individually. 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).