Install now meme

Install now meme DEFAULT

Screenshots

Description

Turn your ideas into Meme magic. Fast.
The MOST POPULAR Memes App Enjoyed by MILLIONS!
Brought to you by Memes.com

This is a completely NEW way of making Memes and connecting with friends. With a few taps you can add captions to pictures or videos and share them with your friends. Being funny & relatable has never been easier.

No need for photoshop or complicated editing apps. All you need is an idea and you can be a great Memer. From idea to publishing everywhere in minutes.

Explore our community, connect with friends, and grow your following. Whether you’re a pop culture fanatic or just looking for a good laugh, Memes has something for everyone.

All the Memes you want. Where you want it.

Some of our Features:

• Discover content from creators around the world and for any interest.
• Message your friends from around the world with our built-in direct messenger.
• Personalized feed of Memes from our community and people you follow.
• Advanced Photo, Video and Gif Meme Maker with a huge library to get you started.
• All the trending and popular Meme Templates and Frames updated daily.
• Powerful Photo and Video Manipulation, including distortion, rewind, slo-mo, deep-fry, • • Freestyle, and much more.
• Easily format and publish anywhere.
• Save your Memes for later inspiration into your own private collection.
• Exclusive stickers and fonts you won’t find anywhere.
• Grow your following with your very own memes profile.
• Brand your original Memes with custom image and text watermarks.

Would you like to get FEATURED inside our app?
Just post your meme with #Memesapp

For even more fun Memes join our community on Instagram and Facebook for special updates, discounts and promos
@Memes

____________

UNLIMITED ACCESS SUBSCRIPTION
• You can subscribe for unlimited access to all features and content offered for purchases within Memes
• Subscriptions are billed monthly, weekly or annually at the rate selected depending on the subscription plan.
• Payment will be charged to your iTunes Account at confirmation of purchase
• Subscription automatically renews at the cost of the chosen package unless auto-renew is turned off at least 24-hours before the end of the current period
• Account will be charged for renewal within 24-hours prior to the end of the current period, and identify the cost of the renewal
• Subscriptions may be managed by the user and auto-renewal may be turned off by going to the user's Account Settings after purchase
• If eligible for free trial and you subscribe before your free trial ends, the rest of your free trial
period will be forfeited as soon as your purchase is confirmed. Subscriptions will start immediately after free trial ends unless cancelled at least 24 hours prior to the end of the trial period.

- Terms of use: https://drive.google.com/open?id=0B2vjItN-_RgPd01VRElERnVZVUk
- Privacy policy: https://drive.google.com/open?id=0B2vjItN-_RgPQWFJQzE4Q05mcms

Version 2.9.21

Few bug fixes and performance improvements

Ratings and Reviews

4.7 out of 5

106K Ratings

Great App for High Quality Memes

This is one of my go-to apps when I want to create a classy-looking meme. It’s very easy to use with tons of options for design, color, and font to generate your creation in a matter of minutes. The memes that I’ve created using this app always receive plenty of “likes”, even from a die-hard Trump supporter (my memes are not flattering to the Donald). Once you’ve created your meme, you can upload it directly to your favorite social media platform or save it to your camera roll. You won’t be disappointed.
***AMENDED - Since the last update, the app keeps wanting me to review it, which I’ve already done. I cannot continue my project until after I’m diverted to the review page. Annoying! I’m taking away a star because of this.

Good, but definitely needs a safety filter

I recently downloaded this app, and it’s great for someone my age or older. I love how easy it is to make memes. You can make them public so everyone can see them and get lots of likes and followers. It’s fun and easy, really an awesome app.
But I think there NEEDS to be some kind of filter, or a setting that makes inappropriate/dirty memes not pop up on the for you page. The first meme I saw when I downloaded this app was absolutely disgusting, I don’t know how it got so many likes because it was racist and homophobic.

There are “popular” memes that make fun of people with disabilities, people of different ethnicities. This is not okay. Posts like that need to be filtered out.
There is so much negativity and hate in a lot of these memes, along with a lot of insensitive, inappropriate images. People have the right to post whatever they want, and I’m not saying they shouldn’t be allowed to post this kind of content, but I’m 15 years old, and I know how to scroll past anything that makes me uncomfortable, and I’m definitely not searching for the memes that just pop up. But I know for a fact that there are always younger viewers on this app. This content is not appropriate for them, and quite frankly, me too. There needs to be a way to enjoy this app without being exposed to all of it. Thank you.

Good but could be better

The app is amazing and I love the availability of being able to post memes I had made. But the issue is that the main app itself has multiple accounts and that’s the only accounts I ever see getting tons of likes. and the only memes I see are from them for that matter. I feel these are getting lots of likes not because they are funny but because people feel like that have to like it because it’s by the app. I have never personally laughed at their posts and I feel the humor is kind of bland. I think it’s also just generally awkward that we have the apps creators or development team or whatever posting and taking up all the space for public memes. I feel we should just have people that got the app instead of the creators for a better experience. The app is amazing overall, but like I said I barely see other people’s posts and is all taken up by the dankmemes channel and others by the creators.

The developer, Meme Plus LLC, indicated that the app’s privacy practices may include handling of data as described below. For more information, see the developer’s privacy policy.

Data Used to Track You

The following data may be used to track you across apps and websites owned by other companies:

  • Contact Info
  • User Content

Data Linked to You

The following data may be collected and linked to your identity:

  • Contact Info
  • User Content
  • Identifiers

Data Not Linked to You

The following data may be collected but it is not linked to your identity:

  • User Content
  • Usage Data
  • Diagnostics

Privacy practices may vary, for example, based on the features you use or your age. Learn More

Information

Seller
Meme Plus LLC

Size
246.2 MB

Category
Entertainment

Compatibility
iPhone
Requires iOS 12.0 or later.
iPad
Requires iPadOS 12.0 or later.
iPod touch
Requires iOS 12.0 or later.
Languages

English, Arabic, Danish, Dutch, Finnish, French, German, Hungarian, Indonesian, Italian, Japanese, Korean, Malay, Persian, Polish, Portuguese, Romanian, Russian, Simplified Chinese, Spanish, Traditional Chinese, Turkish, Vietnamese

Age Rating
12+ Infrequent/Mild Profanity or Crude HumorInfrequent/Mild Mature/Suggestive ThemesInfrequent/Mild Alcohol, Tobacco, or Drug Use or ReferencesInfrequent/Mild Sexual Content and Nudity

Copyright
© Meme Generator LLC

Price
Free

In-App Purchases

  1. Unlock All Premiums$2.99
  2. Unlock All Features$2.99
  3. Access Memes VIP$4.99

Supports

  • Family Sharing

    With Family Sharing set up, up to six family members can use this app.

More By This Developer

You Might Also Like

Sours: https://apps.apple.com/us/app/memes-com/id1175978897

Installing MEME

Table of Contents:


Quick Install (for Linux, OS-X and Cygwin systems)

  1. Type the following commands and then follow the instructions printed by the configure command.
    $ tar zxf meme_VERSION.tar.gz
    $ cd meme_VERSION
    $ ./configure --prefix=$home/meme --with-url=http://meme.nbcr.net/meme
  2. Edit your shell configuration file to add
    $home/meme/bin to your shell's path.

Notes:

  • This installs only the command-line versions of programs. Refer to Installing from a tarball if you wish to install your own MEME Suite Web Application as well.
  • This will overwrite any previously existing $home/meme directory you may have. 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 http://meme.nbcr.net for additional processing when clicked. Refer to the Installing from a tarball if you do not want this feature.

Introduction

The MEME Suite consists of several command line programs and an optional web site. The web site is implemented using static HTML pages, CGI scripts, and SOAP services. The SOAP services are provided through Tomcat, and Opal. Building and installing the command line programs is very straight-forward. Installing the web site requires more detailed configuration information.

Prerequisite software

Most of the software mentioned here is standard on many UNIX systems. To build MEME Suite you will need:

  • Perl (v.5.10.1 or higher) is needed to run some scripts. See http://www.perl.org for download and installation instructions.
  • The following perl modules: (there are others but they are typically already available as part of the Perl installation.)
    • HTML::PullParser
    • HTML::Template
  • Python (v2.5.1 up to v2.7.x) is needed to run some scripts (including Dreme). See http://www.python.org for download and installation instructions.
  • Psyco, the Python Specializing Compiler, is highly recommended because it gives 2 - 3 times speedups for running Dreme. See http://sourceforge.net/projects/psyco/ for download and installation instructions.
  • Bourne compatible shell
  • Make utility
  • C compiler
  • Gzip/gunzip utilities

If you are installing the web site you will also need:

  • A web server supporting CGI. Apache is a common choice.
  • Version 5.0.30 or later of the Apache Tomcat servlet container and web server. Version 5.5.25 is recommended because it supports CGI, and allows Tomcat to host the entire MEME Suite web application. MEME Suite has not been tested with version 6.
  • Version 2 of Opal SOAP wrapper servlet.
  • The following perl modules: (there are others but they are typically already available as part of the Perl installation.)
    • HTTP
    • HTML::PullParser
    • HTML::Template
    • LWP
    • SOAP::Lite
    • XML::Simple

Optional software:

  • Version 2.6.0 or later of the libxml2 library. If this library is not available the MEME Suite will build a copy for its own use, but having this library already installed will greatly speed up the build process.
  • Version 1.1 or later of the libxslt library. If this library is not available the MEME Suite will build a copy for its own use, but having this library already installed will greatly speed up the build process.
  • The convert program from the ImageMagick package is needed to convert logograms from EPS to PNG format .
  • A Linux cluster running Rocks (see http:www.rocksclusters.org ) or similar cluster environment. Rocks provides all the required and optional software.
  • If you want to run parallel version of MEME you will need an MPI implementation and a batch scheduler. For MPI, one of the following: For batch scheduler, one of the following:

[ Top ]


Getting the source

The current version of MEME is 4.5.0 and is available from http://meme.nbcr.net/downloads/.

Note: MEME has undergone many changes in version 4.0.0. It is optimized and configured for running on Linux servers. It hasn't been fully tested on other platforms, and your feedback is greatly appreciated. If you'd like to wait until all the kinks to be worked out before trying the current release, please use the previous version (use version 3.5.7) from http://meme.nbcr.net/downloads/old_versions. Installation instructions for version 3.5.7 are different and are specified in the README file included in the release distribution meme_3.5.7.tar.gz.

The software is distributed as a source tarball meme_VERSION.tar.gz. For each file there is a corresponding file with the MD5 checksum: meme_VERSION.md5sum. When downloading the software, please make sure you download the corresponding checksum file and verify that the checksum information is correct. Depending on a platform and available software, the verification command can be different. Here there are 3 possible ways to do verification:

  1. Using md5sum command, usually available on Linux.
    $ md5sum meme_VERSION.tar.gz
  2. Using md5 command, usually available on Solaris.
    $ md5 meme_VERSION.tar.gz
  3. Using openssl command, usually available on any UNIX.
    $ openssl dgst -md5 meme_VERSION.tar.gz

The output of the command (numerical part) should be exactly the same as one provided in the checksum file. Here is the checksum information for available MEME versions:

[ Top ]


Getting and installing the patches

The distribution may have patches associated with it. They are available from http://meme.nbcr.net/downloads/. Patch files are located in a directory named VERSION.patches, for example, meme_3.5.4.patches. Patch file have names like: VERSION.patch_SERIAL_NO, for example, meme_3.5.4.patch_3.

To install a patch, download the patch file from the URL given above. Then perform the following commands to install it:
$ cp PATCH_FILE VERSION
$ cd VERSION
$ patch -p1 < PATCH_FILE
$ make install
$ make test

For example, to install the first patch to version meme_3.5.4, you would perform the following commands:
$ cp meme_3.5.4.patch_1 meme_3.5.4
$ cd meme_3.5.4
$ patch -p1 < meme_3.5.4.patch_1
$ make install
$ make test

You must install all of the patches for a specific version in serial number order. For example, if you wish to install patch number 3, you must first have installed patches number 1 and 2 for that version. This is easy to do. Just download all the patches for your current version, copy them to your current version's directory, and then install them in order by repeating the patch, command above, with each patch file. You only need to run the install and make test commands once, after the last patch command.

[ Top ]


System Requirements

MEME has been used successfully on the following platforms

  • v 4.0.0
    • Redhat Enterprise Linux, release 5
    • Fedora Linux 7
    • MacOS X 10.5 (Leopard)
    • Cygwin (DLL 1.5.19-4.) running under Windows
  • v 3.5.7
    • Redhat Enterprise Linux, release 4
    • MacOS X 10.4.4 (Tiger)
    • Cygwin (DLL 1.5.19-4.) running under Windows
  • v 3.5.1
    • Redhat Enterprise Linux, release 4
    • MacOS X 10.4.4 (Tiger)
    • Cygwin (DLL 1.5.19-4.) running under Windows
    • SunOS 5.9
  • v 3.5.0
    • SunOS 5.9
    • Redhat Enterprise Linux, release 4

Disk use:

  • Minimal installation including only command line tools: 2.7 MB
  • Full web site (not including sequence databases) 23 MB

[ Top ]


MEME Suite Directories

Installation of MEME Suite will create the following directories:

bin/ db/ etc/ lib/ LOGS/ web/

The directories contain:

bin/
MEME Suite executables and scripts
db/
this directory or DIR specified by --with-db=DIR option is created. Initially, the database directory is empty, and is filled with the sequence databases after running update_db command.
doc/
Supplementary documentation for some of the MEME Suite tools.
etc/
contains the following files
  • db_*.csv - sequence database information listed as comma separated values. Used for running update_db command
  • mast.doc, meme.doc - text files used by a few commands to provide usage info
  • prior1.plib, prior30.plib - these files are used by MEME
lib/
contains common Perl modules
LOGS/
directory for temporary files created by mast or MEME when jobs are submitted via web
web/
contains static HTML and CGI scripts needed for a web-based access to the MEME Suite programs. This directory is only created if the MEME Suite web site is installed.

[ Top ]


Installing from a tarball

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 SVN access please see section Installing from an SVN repository.

Four steps are required to install the MEME Suite from a distribution tarball:

  1. Unzip and untar the distribution
  2. Configure the installation using the configure command.
  3. Build MEME Suite using the make command
  4. Install MEME Suite using the make install command

1. Unzip and untar the distribution:

Use the commands:

$ tar zxf meme_VERSION.tar.gz
$ cd meme_VERSION

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

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

2. Configuring the installation

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:

$ ./configure [parameters here]

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 if you use this command (unless you also install a MEME Suite web server on the same host). This is safe (you won't be able to send your data over the internet accidentally), but not very useful. However, if this is what you want the simplest command is:

$ ./configure

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 NBCR, the simplest configuration command is

$ ./configure --with-url="http://meme.nbcr.net/meme"

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

$ ./configure --prefix=your-install-path --with-url="http://meme.nbcr.net/meme"

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 NBCR. 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 parameters. For example,

$ ./configure \
--prefix=your-install-path \
--enable-build-libxml2 \
--enable-build-libxslt

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

Configuring installation of the MEME Suite Web Application

Four 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 name of the directory where the static HTML pages and CGI scripts should be installed
  • the name of the directory containing the Opal build file for configuring the MEME Suite SOAP service

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 almost certainly want 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 http://ws.nbcr.net/opal2/services. For example,

$ ./configure \
--prefix=your-install-path \
--with-url=url-for-meme-on-your-web-server \
--enable-web

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 http://ws.nbcr.net/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 NBCR server:

$ ./configure \
--prefix=your-install-path \
--with-url=<url-for-meme-on-your-web-server> \
--enable-web=http://ws.nbcr.net/opal2/services/

The parameter with-webdir configures the installation step so that the static HTML pages and CGI scripts will be copied to a particular directory. It defaults to <your-install-path>/web. For example, to force the static HTML and CGI files to be installed in /var/www/meme you would use the command:

$ ./configure \
--prefix=your-install-path \
--with-url=<url-for-meme-on-your-web-server> \
--with-webdir=/var/www/meme

Alternatively you can use a symbolic link to mount the web directory in the web servers directory tree (see step 4 below).

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

You must set the environment variable CATALINA_HOME to the path to the root directory of Tomcat:

$ setenv CATALINA_HOME tomcat-path# for csh, tcsh
or
$ export CATALINA_HOME=tomcat-path# for bash, sh

The parameter enable-webservice is used to specify the location of the ANT build file for Opal.

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

$ ./configure \
--prefix=your-install-path \
--enable-web=http://<base url for your Opal installation>/ \
--enable-webservice=path-to-your-build-opal.xml

3. Building

To build simply type while at the top directory:

$ make

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:

$ make test

If there are errors, the output files from each test will be kept in and can be compared to files in . When tests pass without errors the with the output files is removed automatically.

4. Installing

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

$ make install

Configuring apache web access

This part requires root access to create a symbolic link from the document root directory to the web directory in MEME installation. For example, if meme software is installed in , and the HTTP is , then create a link:
$ ln -s /var/www/html/meme <install.path.here>/web

The URL for web access is typically . Virtual hosts may be configured accordingly.

[ Top ]


Installing from a SVN repository

The process of configuring, building, and installing MEME Suite from an SVN repository is the same as installing from a tarball, but with two extra, initial steps: you must check out the repository, and you must build the configure script.

Access to the SVN 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 SVN access, you can check out the source code with the command:

$ svn checkout svn+ssh://[email protected]/meme/SVNROOT/trunk

Once you've checked out the source code you need to build the configure script:

$ cd trunk
$ ./bootstrap

You can now follow the configuration, building and install steps from installing from a tarball.

[ Top ]


Parallel MEME

By default, will establish if your system has the right software to produce parallel version of MEME. Parallel compilation is disabled if mpicc is not found or if queue status program (part of the SGE or PGS scheduler) is not found. Both must be present on the system. Please see section Prerequisite software for information where to get the software. Currently, parallel version of MEME is known to work with:

MPI distributionsBatch Schedulers
LAM MPISGE
MPICHPBS
  • If your mpicc is installed in non-standard place, use option when running 'configure' to specify the MPI installation directory.
  • If you have a custom version of mpicc (for example, one from Sun HPC ClusterTools) that provides wrappers use option to specify mpicc or its wrapper by full path. The configure looks by default only for names 'mpicc' and 'mpcc'.

Once and are located by configure, the parallel version of MEME, called is compiled and installed automatically via commands and .

MEME currently does not support Open MPI.

[ Top ]


Customizing configuration

Customization is done via the command line arguments to configure. To find out a list and the syntax of the configurable arguments, execute: $ ./configure --help

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

The following table provides a list of parameters available for :

OptionNeeded forDefault value
--prefixProvide the installation location path.$HOME
--enable-build-libxml2Forces MEME Suite to build and use libxml2 code included in MEME Suite distribution.disabled
--enable-build-libxsltForces MEME Suite to build and use libxslt code included in MEME Suite distribution.disabled
--enable-debugProduce an executable with debugging symbols.no debug
--enable-optProduce an executable with optimization.compiler and OS dependent.
--enable-serialProduce only serial version of MEME, do not build parallel version.disabled
--enable-web[=http://url.to.meme/webservice]Build web site applications. Must point it to MEME Suite web services exposed via Opal. Defaults to http://ws.nbcr.net/opal2/services/disabled
--enable-webservice=/path/to/build.xmlDeploy MEME Suite web services utilizing an existing Opal installation. Must point to the build file for the Opal installation.disabled
--with-contact=EMAILSet email of web site administrator.[email protected]$HOSTNAME
--with-convert=path-to-convert-binarySet location of ImageMagick convert application.As found in PATH
--with-db=DBDIRSet path to databases.install-path/db/
--with-dot=path-to-dot-binarySet location of Graphviz dot application.As found in PATH
--with-logs=LOGDIRSet path to logs.install-path/LOGS/
--with-maxtime=TIMESet wall time limit (sec) a web-submitted job started by the web server may use.7200
--with-mpicc=MPICCSet MPICC to use.found mpicc
--with-mpidir=MPIDIRSet MPI installation path.path of found mpicc
--with-perl=path-to-perl-binarySet location of Perl interpreter.As found in PATH
--with-python=path-to-python-binarySet location of Python interpreter.As found in PATH
--with-procs=numprocSet number of processors to use for parallel jobs.2
--with-url=URLSet url for the MEME Suite web site used by buttons on the output of MEME Suite tools.http://$HOSTNAME/meme
--with-blocks-url=URLSet url for the BLOCKMAKER web site.http://blocks.fhcrc.org/blocks-bin/process_blocks.pl
--with-goserver-url=URLSet url for the AMIGO web site.http://amigo.geneontology.org/amigo
--with-webdir=DIRSet path to MEME Suite web site directory.install-path/web/

Note 1: see Parallel MEME section for details.

[ Top ]


Installation Examples

  1. Example 1: installing MEME command line programs without any web components in /opt/meme. Buttons in the MEME output will submit to the default remote server: NBCR.
    $ tar zxf meme_4.3.0.tar.gz
    $ cd meme_4.3.0
    $ ./configure --prefix=/opt/meme
    $ make
    $ make test
    $ make install
  2. Example 2: installing MEME command line programs without any web components in /opt/meme. Buttons in the MEME output will submit to the URL: .
    $ tar zxf meme_4.3.0.tar.gz
    $ cd meme_4.3.0
    $ ./configure --prefix=/opt/meme --with-url=http://meme.imb.uq.edu.au/
    $ make
    $ make test
    $ make install
  3. Example 3: installing MEME command line programs and the static HTML and CGI scripts, but not the SOAP services. The URL for the MEME web site will be and buttons in the MEME output will submit to that URL. This installation will use the MEME SOAP services on http://ws.ncbr.net/opal2/services.
    $ tar zxf meme_4.3.0.tar.gz
    $ cd meme_4.3.0
    $ ./configure --prefix=/home/meme --enable-web --with-url=http://host/meme
    $ make
    $ make test
    $ make install
  4. Example 4: installing the full MEME Suite including all the command line programs, the static HTML and CGI scripts, and the SOAP services. The static HTML, CGI scripts, and SOAP services will all be served by an installation of Tomcat. .
    $ tar zxf meme_4.3.0.tar.gz
    $ cd meme_4.3.0
    $ export CATALINA_HOME=/home/meme/tomcat
    $ ./configure \
    --prefix=/home/meme \
    --enable-web=http://host:8080/opal/services
    --enable-webservice=/home/meme/opal/build.xml \
    --with-url=http://host:8080/meme \
    --with-webdir=/home/meme/tomcat/webapps/meme
    $ make
    $ make test
    $ make install
  5. Example 5: installing the full MEME Suite including all the command line programs, the static HTML and CGI scripts, and the SOAP services. The static HTML, and CGI scripts will be served by an APACHE web server. The SOAP services will all be provided by a separate installation of Tomcat.
    $ tar zxf meme_4.3.0.tar.gz
    $ cd meme_4.3.0
    $ export CATALINA_HOME=/home/meme/tomcat
    $ ./configure \
    --prefix=/home/meme \
    --enable-web=http://host:8080/opal/services
    --enable-webservice=/home/meme/opal/build.xml \
    --with-url=http://host/meme \
    --with-webdir=/home/meme/Sites/meme
    $ make
    $ make test
    $ make install

[ Top ]


Setting Up MEME Web Application Under Tomcat

Note: This procedure was tested with Tomcat 5.0.30.

1. In $CATALINA_HOME/webapps, make a symbolic link to the MEME web installation directory. For example
$ cd $CATALINA_HOME/webapps
$ ln -s $MEME_INSTALL_DIR/web meme

2. In $CATALINA_HOME/conf/Catalina/localhost, create a new file meme.xml with the following contents.
<Context path="/meme" docBase="meme" debug="0" allowLinking="true">
</Context>

3. In $CATALINA_HOME/conf/web.xml, uncomment the block of code just below "Common Gateway Includes (CGI) processing servlet, which supports...". Set param-value to cgi-bin. In addition, uncomment the block of code right below "The mapping for the CGI Gateway servlet".

4. Rename $CATALINA_HOME/server/lib/servlets-cgi.renametojar to $CATALINA_HOME/server/lib/servlets-cgi.jar.

5. Restart Tomcat.

[ Top ]


Uninstalling

You can unistall MEME Suite by giving the command:
$ make uninstall
in the root of the build directory. This will remove all the files installed for the MEME Suite, but won't remove any directories that may have been created.

[ Top ]


Using MEME Suite

Set the environment variable PATH to newly installed MEME Suite executables:
$ setenv PATH your-install-path/bin:${PATH}# for csh, tcsh
or
$ export PATH=your-install-path/bin:$PATH# for bash, sh

[ Top ]


Running regression tests

There is a suit of tests that can be run to test MEME Suite output against known output. These tests can be run during the installation process. A quick "smoke test" can be run using the command:
$ make test
A more complete set of tests can be run from the subdirectory of the build directory:
$ cd tests
$ ../scripts/runtests
This full set of tests can take a long time to run. The output files from the tests go into the newly created directory . If the tests pass without errors this directory with its output files will be deleted. If there are errors the output files are kept and can be compared to files in tests.

[ Top ]


Installing sequence databases

If you have installed MEME Suite web site (using the --enable-web option in the ./configure command), you may optionally define a collection of sequence databases. This will define what sequence databases the associated MEME Suite web services will maintain and allow users to search. If you do not do this, you will not be able to use the sequence search tools on your website.

  1. Firstly, you must create the list of sequence databases on the web site using the commands:


    $ cd etc
    $ get_db_csv -db GENBANK -class Bacteria > db_genbank_bacteria.csv
    $ get_db_csv -db GENBANK -class Fungi > db_genbank_fungi.csv
    $ get_db_csv -db ENSEMBL > db_ensembl.csv
    $ get_db_csv -db ENSEMBL_ABINITIO > db_ensembl_abinitio.csv
    $ get_db_csv -db UPSTREAM > db_upstream.csv
    $ cat db_general.csv db_other_genomes.csv db_ensembl.csv db_ensembl_abinitio.csv db_genbank_fungi.csv db_genbank_bacteria.csv db_upstream.csv > fasta_db.csv
    $ make install

    You should rerun the above commands periodically in order to have the latest list of available sequence databases.

    You can also edit the fasta_db.csv file to add or remove sequence databases. (Place a "#" in the first position of a line to remove a sequence database.) Alternatively, you can create your own fasta_db.csv by hand using a spreadsheet program. The meaning of each column is given in the first line of each of the db_*.csv files included in the distribution.

  2. Next you must update (download) the sequence databases on the MEME Suite web services host (where you installed the web services using the --enable-webservice option in the ./configure command).

    The possible commands to update the sequence databases are:
    $ update_db > dblog.txt
    $ update_db -upstream > dblog.txt
    $ update_db -upstream -noclobber > dblog.txt
    These commands update, respectively, 1) all sequence databases that do not end with the suffix '_upstream'; or 2) all sequence databases including '_upstream' ones; or 3) all sequence databases plus '_upstream' ones that have not yet been downloaded. Note that to use '-upstream' you must create the link 'your-install-path/lib/perl/RSATWS'. This link should point to the RSATWS perl module library available from http://rsat.scmbb.ulb.ac.be/rsat/web_services/RSATWS.tar.gz.

    The resulting files in the db/ directory may be many gigabytes, depending on the contents of the fasta_db.csv file on the web site host (not the one on the web services host). It can take time to download all the sequence databases, and the connections to some sites from which files are downloaded may be not always available. Check the output of the script (dblog.txt) for error messages. If there are errors, the command to install the sequence databases will need to be repeated. The script will skip downloading 'normal' sequence databases that are current with the database source, and 'upstream' sequence databases that have already been downloaded if '-upstream -noclobber' is specified.

    In order to keep the sequence databases current, you can place one of the above 'update_db' commands in a chron job that runs at regular intervals.

[ Top ]


Installing GOMO databases

GOMO uses additional databases which need to be downloaded and installed.

  1. Download databases for GOMO from here.
  2. Extract the databases from the gziped tar:
    tar xzf gomo_databases.X.tgz
    where "X" is the version number of the GOMO databases file
  3. Copy the file gomo_databases/gomo_db.csv to the source etc directory and proceed though the normal installation steps until you have run:
    make install
    If you have already done this step just run "make install" again.
  4. Move the extracted databases folder (or create a soft link) into the installed db/ directory ensuring that the folder (or soft link) in the db/ directory is named gomo_databases.

[ Top ]


Installing motif databases

TOMTOM uses additional databases which need to be downloaded and installed.

  1. Download the motif databases from here.
  2. Extract the databases from the gziped tar:
    tar xzf motif_databases.X.tgz
    where "X" is the version number of the motif databases file
  3. Copy the file motif_databases/motif_db.csv to the source etc directory and proceed though the normal installation steps until you have run:
    make install
    If you have already done this step just run "make install" again.
  4. Move the extracted databases folder (or create a soft link) into the installed db/ directory ensuring that the folder (or soft link) in the db/ directory is named motif_databases.

Note:Due to copyright restrictions, some motif databases may be absent from the file you downloaded in step 1. You may "comment out" the line in the gomo_databases/motif_db.csv file for a missing database by adding a "#" in front of the line for that databases using a text editor. This will inactivate that motif database. Alternatively, if you own a license for a missing database, you can convert the database to MEME format using a command-line script provided with the MEME Suite. These scripts are documented under "motif database conversion utilities", and have names that begin with the motif database name and end with 2meme.

[ Top ]


Known issues

    [ Top ]


    Reporting problems

    Make sure first that you really have a problem:

    • 1. Check your environment
      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?
    • Look for the answers.
      Check the INSTALL and README files that came with the distribution. Check the MEME user forum if your problem has been reported and there was a solution. Check the release notes for possible bug fixes and other version-dependent changes.
    • Are you asking in the right place?
      If your problems are related to the prerequisite software installation, your OS, or compiler, check relevant mailing lists, do Google search, talk to your sysadmin.
    • Verify what you did.
      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.
    • Report the problem.
      If all fails and you still have the problem, go ahead and email to [email protected] Here is a guiding list of what to put in your email:
      • Use meaningful and specific email headers
      • Write clearly and be precise about your problem. Give as much information as possible, yet avoid dumping large volumes of data.
      • Essential information to include: your OS version, the software version you are trying to install, your compiler version, autoconf version ...
      • Describe the exact problem symptoms, and whether they are reproducible. Provide the relevant output from running or that indicates what the error was.

    [ Top ]

    Sours: http://mtweb.cs.ucl.ac.uk/mus/MEME/meme_4.7.0/doc/meme-install.html
    1. Furniture end caps
    2. Intense life quotes
    3. Magnetic silicone bracelet
    4. Spartan shield vector

    Installing MEME

    Table of Contents:


    Quick Install (for Linux, OS-X and Cygwin systems)

    1. Type the following commands and then follow the instructions printed by the configure command.
      $ tar zxf meme_VERSION.tar.gz
      $ cd meme_VERSION
      $ ./configure --prefix=$home/meme --with-url=http://meme.nbcr.net/meme
    2. Edit your shell configuration file to add
      $home/meme/bin to your shell's path.

    Notes:

    • This installs only the command-line versions of programs. Refer to Installing from a tarball if you wish to install your own MEME Suite Web Application as well.
    • This will overwrite any previously existing $home/meme directory you may have. 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 http://meme.nbcr.net for additional processing when clicked. Refer to the Installing from a tarball if you do not want this feature.

    Introduction

    The MEME Suite consists of several command line programs and an optional web site. The web site is implemented using static HTML pages, CGI scripts, and SOAP services. The SOAP services are provided through Tomcat, and Opal. Building and installing the command line programs is very straight-forward. Installing the web site requires more detailed configuration information.

    Prerequisite software

    Most of the software mentioned here is standard on many UNIX systems. To build MEME Suite you will need:

    • Perl (v.5.6.1 or higher) is needed to run some scripts. See http://www.perl.org for download and installation instructions.
    • Bourne compatible shell
    • Make utility
    • C compiler
    • Gzip/gunzip utilities

    If you are installing the web site you will also need:

    • A web server supporting CGI. Apache is a common choice.
    • Version 5.0.30 or later of the Apache Tomcat servlet container and web server. Version 5.5.25 is recommended because it supports CGI, and allows Tomcat to host the entire MEME Suite web application. MEME Suite has not been tested with version 6.
    • Version 2 of Opal SOAP wrapper servlet.
    • The following perl modules: (these will be typically already be available as part of the Perl installation.)
      • CGI
      • File::Basename
      • File::Find.
      • File::Temp
      • FileHandle
      • HTTP
      • LWP
      • MIME::Base64
      • Net::FTP
      • SOAP::Lite
      • XML::Simple

    Optional software:

    • Version 2.6.0 or later of the libxml2 library. If this library is not available the MEME Suite will build a copy for its own use, but having this library already installed will greatly speed up the build process.
    • Version 1.1 or later of the libxslt library. If this library is not available the MEME Suite will build a copy for its own use, but having this library already installed will greatly speed up the build process.
    • The convert program from the ImageMagick package is needed to convert logograms from EPS to PNG format .
    • A Linux cluster running Rocks (see http:www.rocksclusters.org ) or similar cluster environment. Rocks provides all the required and optional software.
    • If you want to run parallel version of MEME you will need an MPI implementation and a batch scheduler. For MPI, one of the following: For batch scheduler, one of the following:

    [ Top ]


    Getting the source

    The current version of MEME is 4.1.1 and is available from http://meme.nbcr.net/downloads/.

    Note: MEME has undergone many changes in version 4.0.0. It is optimized and configured for running on Linux servers. It hasn't been fully tested on other platforms, and your feedback is greatly appreciated. If you'd like to wait until all the kinks to be worked out before trying the current release, please use the previous version (use version 3.5.7) from http://meme.nbcr.net/downloads/old_versions. Installation instructions for version 3.5.7 are different and are specified in the README file included in the release distribution meme_3.5.7.tar.gz.

    The software is distributed as a source tarball meme_VERSION.tar.gz. For each file there is a corresponding file with the MD5 checksum: meme_VERSION.md5sum. When downloading the software, please make sure you download the corresponding checksum file and verify that the checksum information is correct. Depending on a platform and available software, the verification command can be different. Here there are 3 possible ways to do verification:

    1. Using md5sum command, usually available on Linux.
      $ md5sum meme_VERSION.tar.gz
    2. Using md5 command, usually available on Solaris.
      $ md5 meme_VERSION.tar.gz
    3. Using openssl command, usually available on any UNIX.
      $ openssl dgst -md5 meme_VERSION.tar.gz

    The output of the command (numerical part) should be exactly the same as one provided in the checksum file. Here is the checksum information for available MEME versions:

    [ Top ]


    Getting and installing the patches

    The distribution may have patches associated with it. They are available from http://meme.nbcr.net/downloads/. Patch files are located in a directory named VERSION.patches, for example, meme_3.5.4.patches. Patch file have names like: VERSION.patch_SERIAL_NO, for example, meme_3.5.4.patch_3.

    To install a patch, download the patch file from the URL given above. Then perform the following commands to install it:
    $ cp PATCH_FILE VERSION
    $ cd VERSION
    $ patch -p1 < PATCH_FILE
    $ make install
    $ make test

    For example, to install the first patch to version meme_3.5.4, you would perform the following commands:
    $ cp meme_3.5.4.patch_1 meme_3.5.4
    $ cd meme_3.5.4
    $ patch -p1 < meme_3.5.4.patch_1
    $ make install
    $ make test

    You must install all of the patches for a specific version in serial number order. For example, if you wish to install patch number 3, you must first have installed patches number 1 and 2 for that version. This is easy to do. Just download all the patches for your current version, copy them to your current version's directory, and then install them in order by repeating the patch, command above, with each patch file. You only need to run the install and make test commands once, after the last patch command.

    [ Top ]


    System Requirements

    MEME has been used successfully on the following platforms

    • v 4.0.0
      • Redhat Enterprise Linux, release 5
      • Fedora Linux 7
      • MacOS X 10.5 (Leopard)
      • Cygwin (DLL 1.5.19-4.) running under Windows
    • v 3.5.7
      • Redhat Enterprise Linux, release 4
      • MacOS X 10.4.4 (Tiger)
      • Cygwin (DLL 1.5.19-4.) running under Windows
    • v 3.5.1
      • Redhat Enterprise Linux, release 4
      • MacOS X 10.4.4 (Tiger)
      • Cygwin (DLL 1.5.19-4.) running under Windows
      • SunOS 5.9
    • v 3.5.0
      • SunOS 5.9
      • Redhat Enterprise Linux, release 4

    Disk use:

    • Minimal installation including only command line tools: 2.7 MB
    • Full web site (not including sequence databases) 23 MB

    [ Top ]


    MEME Suite Directories

    Installation of MEME Suite will create the following directories:

    bin/ db/ etc/ lib/ LOGS/ web/

    The directories contain:

    bin/
    MEME Suite executables and scripts
    db/
    this directory or DIR specified by --with-db=DIR option is created. Initially, the database directory is empty, and is filled with the sequence databases after running update_db command.
    doc/
    Supplementary documentation for some of the MEME Suite tools.
    etc/
    contains the following files
    • db_*.csv - sequence database information listed as comma separated values. Used for running update_db command
    • mast.doc, meme.doc - text files used by a few commands to provide usage info
    • prior1.plib, prior30.plib - these files are used by MEME
    lib/
    contains common Perl modules
    LOGS/
    directory for temporary files created by mast or MEME when jobs are submitted via web
    web/
    contains static HTML and CGI scripts needed for a web-based access to the MEME Suite programs. This directory is only created if the MEME Suite web site is installed.

    [ Top ]


    Installing from a tarball

    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 SVN access please see section Installing from an SVN repository.

    Four steps are required to install the MEME Suite from a distribution tarball:

    1. Unzip and untar the distribution
    2. Configure the installation using the configure command.
    3. Build MEME Suite using the make command
    4. Install MEME Suite using the make install command

    1. Unzip and untar the distribution:

    Use the commands:

    $ tar zxf meme_VERSION.tar.gz
    $ cd meme_VERSION

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

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

    2. Configuring the installation

    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:

    $ ./configure [parameters here]

    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 if you use this command (unless you also install a MEME Suite web server on the same host). This is safe (you won't be able to send your data over the internet accidentally), but not very useful. However, if this is what you want the simplest command is:

    $ ./configure

    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 NBCR, the simplest configuration command is

    $ ./configure --with-url="http://meme.nbcr.net/meme"

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

    $ ./configure --prefix=your-install-path --with-url="http://meme.nbcr.net/meme"

    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 NBCR. 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 parameters. For example,

    $ ./configure \
    --prefix=your-install-path \
    --enable-build-libxml2 \
    --enable-build-libxslt

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

    Configuring installation of the MEME Suite Web Application

    Four 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 name of the directory where the static HTML pages and CGI scripts should be installed
    • the name of the directory containing the Opal build file for configuring the MEME Suite SOAP service

    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 almost certainly want 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 http://ws.nbcr.net/opal2/services. For example,

    $ ./configure \
    --prefix=your-install-path \
    --with-url=url-for-meme-on-your-web-server \
    --enable-web

    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 http://ws.nbcr.net/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 NBCR server:

    $ ./configure \
    --prefix=your-install-path \
    --with-url=<url-for-meme-on-your-web-server> \
    --enable-web=http://ws.nbcr.net/opal2/services/

    The parameter with-webdir configures the installation step so that the static HTML pages and CGI scripts will be copied to a particular directory. It defaults to <your-install-path>/web. For example, to force the static HTML and CGI files to be installed in /var/www/meme you would use the command:

    $ ./configure \
    --prefix=your-install-path \
    --with-url=<url-for-meme-on-your-web-server> \
    --with-webdir=/var/www/meme

    Alternatively you can use a symbolic link to mount the web directory in the web servers directory tree (see step 4 below).

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

    You must set the environment variable CATALINA_HOME to the path to the root directory of Tomcat:

    $ setenv CATALINA_HOME tomcat-path# for csh, tcsh
    or
    $ export CATALINA_HOME=tomcat-path# for bash, sh

    The parameter enable-webservice is used to specify the location of the ANT build file for Opal.

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

    $ ./configure \
    --prefix=your-install-path \
    --enable-web=http://<base url for your Opal installation>/ \
    --enable-webservice=path-to-your-build-opal.xml

    3. Building

    To build simply type while at the top directory:

    $ make

    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:

    $ make test

    If there are errors, the output files from each test will be kept in and can be compared to files in . When tests pass without errors the with the output files is removed automatically.

    4. Installing

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

    $ make install

    Configuring apache web access

    This part requires root access to create a symbolic link from the document root directory to the web directory in MEME installation. For example, if meme software is installed in , and the HTTP is , then create a link:
    $ ln -s /var/www/html/meme <install.path.here>/web

    The URL for web access is typically . Virtual hosts may be configured accordingly.

    [ Top ]


    Installing from a SVN repository

    The process of configuring, building, and installing MEME Suite from an SVN repository is the same as installing from a tarball, but with two extra, initial steps: you must check out the repository, and you must build the configure script.

    Access to the SVN 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 SVN access, you can check out the source code with the command:

    $ svn checkout svn+ssh://[email protected]/meme/SVNROOT/trunk

    Once you've checked out the source code you need to build the configure script:

    $ cd trunk
    $ ./bootstrap

    You can now follow the configuration, building and install steps from installing from a tarball.

    [ Top ]


    Parallel MEME

    By default, will establish if your system has the right software to produce parallel version of MEME. Parallel compilation is disabled if mpicc is not found or if queue status program (part of the SGE or PGS scheduler) is not found. Both must be present on the system. Please see section Prerequisite software for information where to get the software. Currently, parallel version of MEME is known to work with:

    MPI distributionsBatch Schedulers
    LAM MPISGE
    MPICHPBS
    • If your mpicc is installed in non-standard place, use option when running 'configure' to specify the MPI installation directory.
    • If you have a custom version of mpicc (for example, one from Sun HPC ClusterTools) that provides wrappers use option to specify mpicc or its wrapper by full path. The configure looks by default only for names 'mpicc' and 'mpcc'.

    Once and are located by configure, the parallel version of MEME, called is compiled and installed automatically via commands and .

    MEME currently does not support Open MPI.

    [ Top ]


    Customizing configuration

    Customization is done via the command line arguments to configure. To find out a list and the syntax of the configurable arguments, execute: $ ./configure --help

    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

    The following table provides a list of parameters available for :

    OptionNeeded forDefault value
    --prefixProvide the installation location path.$HOME
    --enable-build-libxml2Forces MEME Suite to build and use libxml2 code included in MEME Suite distribution.disabled
    --enable-build-libxsltForces MEME Suite to build and use libxslt code included in MEME Suite distribution.disabled
    --enable-debugProduce an executable with debugging symbols.no debug
    --enable-optProduce an executable with optimization.compiler and OS dependent.
    --enable-serialProduce only serial version of MEME, do not build parallel version.disabled
    --enable-web[=http://url.to.meme/webservice]Build web site applications. Must point it to MEME Suite web services exposed via Opal. Defaults to http://ws.nbcr.net/opal2/services/disabled
    --enable-webservice=/path/to/build.xmlDeploy MEME Suite web services utilizing an existing Opal installation. Must point to the build file for the Opal installation.disabled
    --with-contact=EMAILSet email of web site administrator.[email protected]$HOSTNAME
    --with-convert=path-to-convert-binarySet location of ImageMagick convert application.As found in PATH
    --with-db=DBDIRSet path to databases.install-path/db/
    --with-dot=path-to-dot-binarySet location of Graphviz dot application.As found in PATH
    --with-logs=LOGDIRSet path to logs.install-path/LOGS/
    --with-maxtime=TIMESet wall time limit (sec) a web-submitted job started by the web server may use.7200
    --with-mpicc=MPICCSet MPICC to use.found mpicc
    --with-mpidir=MPIDIRSet MPI installation path.path of found mpicc
    --with-procs=numprocSet number of processors to use for parallel jobs.2
    --with-url=URLSet url for the MEME Suite web site used by buttons on the output of MEME Suite tools.http://$HOSTNAME/meme
    --with-blocks-url=URLSet url for the BLOCKMAKER web site.http://blocks.fhcrc.org/blocks-bin/process_blocks.pl
    --with-goserver-url=URLSet url for the AMIGO web site.http://amigo.geneontology.org/amigo
    --with-webdir=DIRSet path to MEME Suite web site directory.install-path/web/

    Note 1: see Parallel MEME section for details.

    [ Top ]


    Installation Examples

    1. Example 1: installing MEME command line programs without any web components in /opt/meme. Buttons in the MEME output will submit to the default remote server: NBCR.
      $ tar zxf meme_4.3.0.tar.gz
      $ cd meme_4.3.0
      $ ./configure --prefix=/opt/meme
      $ make
      $ make test
      $ make install
    2. Example 2: installing MEME command line programs without any web components in /opt/meme. Buttons in the MEME output will submit to the URL: .
      $ tar zxf meme_4.3.0.tar.gz
      $ cd meme_4.3.0
      $ ./configure --prefix=/opt/meme --with-url=http://meme.imb.uq.edu.au/
      $ make
      $ make test
      $ make install
    3. Example 3: installing MEME command line programs and the static HTML and CGI scripts, but not the SOAP services. The URL for the MEME web site will be and buttons in the MEME output will submit to that URL. This installation will use the MEME SOAP services on http://ws.ncbr.net/opal2/services.
      $ tar zxf meme_4.3.0.tar.gz
      $ cd meme_4.3.0
      $ ./configure --prefix=/home/meme --enable-web --with-url=http://host/meme
      $ make
      $ make test
      $ make install
    4. Example 4: installing the full MEME Suite including all the command line programs, the static HTML and CGI scripts, and the SOAP services. The static HTML, CGI scripts, and SOAP services will all be served by an installation of Tomcat. .
      $ tar zxf meme_4.3.0.tar.gz
      $ cd meme_4.3.0
      $ export CATALINA_HOME=/home/meme/tomcat
      $ ./configure \
      --prefix=/home/meme \
      --enable-web=http://host:8080/opal/services
      --enable-webservice=/home/meme/opal/build.xml \
      --with-url=http://host:8080/meme \
      --with-webdir=/home/meme/tomcat/webapps/meme
      $ make
      $ make test
      $ make install
    5. Example 5: installing the full MEME Suite including all the command line programs, the static HTML and CGI scripts, and the SOAP services. The static HTML, and CGI scripts will be served by an APACHE web server. The SOAP services will all be provided by a separate installation of Tomcat.
      $ tar zxf meme_4.3.0.tar.gz
      $ cd meme_4.3.0
      $ export CATALINA_HOME=/home/meme/tomcat
      $ ./configure \
      --prefix=/home/meme \
      --enable-web=http://host:8080/opal/services
      --enable-webservice=/home/meme/opal/build.xml \
      --with-url=http://host/meme \
      --with-webdir=/home/meme/Sites/meme
      $ make
      $ make test
      $ make install

    [ Top ]


    Setting Up MEME Web Application Under Tomcat

    Note: This procedure was tested with Tomcat 5.0.30.

    1. In $CATALINA_HOME/webapps, make a symbolic link to the MEME web installation directory. For example
    $ cd $CATALINA_HOME/webapps
    $ ln -s $MEME_INSTALL_DIR/web meme

    2. In $CATALINA_HOME/conf/Catalina/localhost, create a new file meme.xml with the following contents.
    <Context path="/meme" docBase="meme" debug="0" allowLinking="true">
    </Context>

    3. In $CATALINA_HOME/conf/web.xml, uncomment the block of code just below "Common Gateway Includes (CGI) processing servlet, which supports...". Set param-value to cgi-bin. In addition, uncomment the block of code right below "The mapping for the CGI Gateway servlet".

    4. Rename $CATALINA_HOME/server/lib/servlets-cgi.renametojar to $CATALINA_HOME/server/lib/servlets-cgi.jar.

    5. Restart Tomcat.

    [ Top ]


    Uninstalling

    You can unistall MEME Suite by giving the command:
    $ make uninstall
    in the root of the build directory. This will remove all the files installed for the MEME Suite, but won't remove any directories that may have been created.

    [ Top ]


    Using MEME Suite

    Set the environment variable PATH to newly installed MEME Suite executables:
    $ setenv PATH your-install-path/bin:${PATH}# for csh, tcsh
    or
    $ export PATH=your-install-path/bin:$PATH# for bash, sh

    [ Top ]


    Running regression tests

    There is a suit of tests that can be run to test MEME Suite output against known output. These tests can be run during the installation process. A quick "smoke test" can be run using the command:
    $ make test
    A more complete set of tests can be run from the subdirectory of the build directory:
    $ cd tests
    $ ../scripts/runtests
    This full set of tests can take a long time to run. The output files from the tests go into the newly created directory . If the tests pass without errors this directory with its output files will be deleted. If there are errors the output files are kept and can be compared to files in tests.

    [ Top ]


    Installing sequence databases

    If you have installed MEME Suite web site (using the --enable-web option in the ./configure command), you may optionally define a collection of sequence databases. This will define what sequence databases the associated MEME Suite web services will maintain and allow users to search. If you do not do this, you will not be able to use the sequence search tools on your website.

    1. Firstly, you must create the list of sequence databases on the web site using the commands:


      $ cd etc
      $ get_db_csv -db GENBANK -class Bacteria > db_genbank_bacteria.csv
      $ get_db_csv -db GENBANK -class Fungi > db_genbank_fungi.csv
      $ get_db_csv -db ENSEMBL > db_ensembl.csv
      $ get_db_csv -db ENSEMBL_ABINITIO > db_ensembl_abinitio.csv
      $ get_db_csv -db UPSTREAM > db_upstream.csv
      $ cat db_general.csv db_other_genomes.csv db_ensembl.csv db_ensembl_abinitio.csv db_genbank_fungi.csv db_genbank_bacteria.csv db_upstream.csv > fasta_db.csv
      $ make install

      You should rerun the above commands periodically in order to have the latest list of available sequence databases.

      You can also edit the fasta_db.csv file to add or remove sequence databases. (Place a "#" in the first position of a line to remove a sequence database.) Alternatively, you can create your own fasta_db.csv by hand using a spreadsheet program. The meaning of each column is given in the first line of each of the db_*.csv files included in the distribution.

    2. Next you must update (download) the sequence databases on the MEME Suite web services host (where you installed the web services using the --enable-webservice option in the ./configure command).

      The possible commands to update the sequence databases are:
      $ update_db > dblog.txt
      $ update_db -upstream > dblog.txt
      $ update_db -upstream -noclobber > dblog.txt
      These commands update, respectively, 1) all sequence databases that do not end with the suffix '_upstream'; or 2) all sequence databases including '_upstream' ones; or 3) all sequence databases plus '_upstream' ones that have not yet been downloaded. Note that to use '-upstream' you must create the link 'your-install-path/lib/perl/RSATWS'. This link should point to the RSATWS perl module library available from http://rsat.scmbb.ulb.ac.be/rsat/web_services/RSATWS.tar.gz.

      The resulting files in the db/ directory may be many gigabytes, depending on the contents of the fasta_db.csv file on the web site host (not the one on the web services host). It can take time to download all the sequence databases, and the connections to some sites from which files are downloaded may be not always available. Check the output of the script (dblog.txt) for error messages. If there are errors, the command to install the sequence databases will need to be repeated. The script will skip downloading 'normal' sequence databases that are current with the database source, and 'upstream' sequence databases that have already been downloaded if '-upstream -noclobber' is specified.

      In order to keep the sequence databases current, you can place one of the above 'update_db' commands in a chron job that runs at regular intervals.

    [ Top ]


    Installing GOMO databases

    GOMO uses additional databases which need to be downloaded and installed.

    1. Download databases for GOMO from here.
    2. Extract the databases from the gziped tar:
      tar xzf gomo_databases.X.tgz
      where "X" is the version number of the GOMO databases file
    3. Copy the file gomo_databases/gomo_db.csv to the source etc directory and proceed though the normal installation steps until you have run:
      make install
      If you have already done this step just run "make install" again.
    4. Move the extracted databases folder (or create a soft link) into the installed db/ directory ensuring that the folder (or soft link) in the db/ directory is named gomo_databases.

    [ Top ]


    Installing motif databases

    TOMTOM uses additional databases which need to be downloaded and installed.

    1. Download the motif databases from here.
    2. Extract the databases from the gziped tar:
      tar xzf motif_databases.X.tgz
      where "X" is the version number of the motif databases file
    3. Copy the file motif_databases/motif_db.csv to the source etc directory and proceed though the normal installation steps until you have run:
      make install
      If you have already done this step just run "make install" again.
    4. Move the extracted databases folder (or create a soft link) into the installed db/ directory ensuring that the folder (or soft link) in the db/ directory is named motif_databases.

    Note:Due to copyright restrictions, some motif databases may be absent from the file you downloaded in step 1. You may "comment out" the line in the gomo_databases/motif_db.csv file for a missing database by adding a "#" in front of the line for that databases using a text editor. This will inactivate that motif database. Alternatively, if you own a license for a missing database, you can convert the database to MEME format using a command-line script provided with the MEME Suite. These scripts are documented under "motif database conversion utilities", and have names that begin with the motif database name and end with 2meme.

    [ Top ]


    Known issues

      [ Top ]


      Reporting problems

      Make sure first that you really have a problem:

      • 1. Check your environment
        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?
      • Look for the answers.
        Check the INSTALL and README files that came with the distribution. Check the MEME user forum if your problem has been reported and there was a solution. Check the release notes for possible bug fixes and other version-dependent changes.
      • Are you asking in the right place?
        If your problems are related to the prerequisite software installation, your OS, or compiler, check relevant mailing lists, do Google search, talk to your sysadmin.
      • Verify what you did.
        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.
      • Report the problem.
        If all fails and you still have the problem, go ahead and email to [email protected] Here is a guiding list of what to put in your email:
        • Use meaningful and specific email headers
        • Write clearly and be precise about your problem. Give as much information as possible, yet avoid dumping large volumes of data.
        • Essential information to include: your OS version, the software version you are trying to install, your compiler version, autoconf version ...
        • Describe the exact problem symptoms, and whether they are reproducible. Provide the relevant output from running or that indicates what the error was.

      [ Top ]

      Sours: https://pgfe.umassmed.edu/meme/doc/meme-install.html

      The MEME Suite

      Motif-based sequence analysis tools

      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 SOAP services. The SOAP services are provided through Tomcat and Opal, 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:


      Quick Install (for Linux, OS X and Cygwin systems)

      1. Download the software from https://meme-suite.org/doc/download.html/
      2. Type the following commands

        tar zxf meme-.tar.gz cd meme- ./configure --prefix=$HOME/meme --enable-build-libxml2 --enable-build-libxslt make make test make install

      3. Edit your shell configuration file to add and to your shell's path. This can often be done by editing the file named to add the following line:

        export PATH=$HOME/meme/bin:$HOME/meme/libexec/meme-:$PATH

      Notes:

      • This installs only the command-line versions of programs. Refer to Installing from a tarball 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 https://meme-suite.org/meme for additional processing when clicked. Refer to the Installing from a tarball if you do not want this feature.
      • The 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 Prerequisite software installed. You will want to read that section of this manual and run the script as described there to see what you may be missing.

      [ Top ]


      Prerequisite software

      Most of the software mentioned here is standard on many UNIX-like systems. To build MEME Suite with just the command-line tools you will need:

      Optional software includes:

      Additionally if you want to install MEME Suite web server you will also need:

      Perl (version 5.16 or higher)

      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 directory of the MEME Suite installation files.

      cd scripts perl dependencies.pl

      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:

      Checking Required Perl Modules: Math::CDF missing. 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.

      sudo cpan Math::CDF

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

      sudo apt-get install libexpat1-dev

      Python (version 2.7.x or 3.x)

      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.

      zlib

      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:

      sudo port install zlib

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

      sudo apt-get install zlib1g-dev

      Ghostscript

      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.

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

      sudo port install ghostscript

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

      Assorted Common Utilities

      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:

      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:

      sudo port install autoconf sudo port install automake sudo port install libtool

      Ubuntu and related distributions can use the install commands:

      sudo apt-get install autoconf sudo apt-get install automake sudo apt-get install libtool

      Installing command-line tools on OS X

      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.

      MacPorts on OS X [optional]

      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

      port list 'tomcat*'

      and MacPorts will tell you if it can install the package.

      MPI [recommended]

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

      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:

      sudo port install openmpi

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

      sudo port select --set mpi openmpi-mp-fortran

      libxml2 (version 2.6.0 or later), libxslt (version 1.1 or later) & libexslt [optional]

      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 Development Kit Standard Edition (version 6 or higher) [for web server or developer only]

      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:

      sudo apt-get install default-jdk

      Apache Ant [for web server or developer only]

      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 script is run.

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

      sudo port install apache-ant

      Ubuntu and related distributions can use the install command:

      sudo apt-get install ant

      Apache Tomcat (version 7 or higher) [for web server only]

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

      Opal (version 2.5) [for web server only]

      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.

      Batch Scheduler [for web server on a compute cluster]

      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:

      [ Top ]


      Getting the source

      Releases of the MEME Suite are available from https://meme-suite.org/doc/download.html/ (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 available:

      • 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.

      [ Top ]


      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 https://meme-suite.org/doc/download.html/ (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:

      cd meme- patch -p1 -i ../PATH_TO_PATCH/patch__1 make make test make install

      If you have more than one patch to install simply group all the patch commands together and only run the make commands once.

      Some patches will require "-p0" to be passed as an argument instead of "-p1" but the readme will specify which to use.

      [ Top ]


      MEME Suite Directories

      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 which contains the motif databases, a folder which contains the gomo databases and a folder 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 in the directory and the SQLite library in the directory .

      [ Top ]


      Installing from a tarball

      If you're setting up a web-accessible 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 Installing from an Mecurial repository.

      Four steps are required to install the MEME Suite from a distribution tarball:

      1. Unzip and untar the distribution
      2. Configure the installation using the command:
      3. Build MEME Suite using the command:
      4. Test the MEME Suite build by using the command: .
        Note: You can run more extensive (and much slower) tests using the command:
      5. Install MEME Suite using the command:

      1. Unzip and untar the distribution:

      For example for release you should use the commands:

      tar zxf meme-.tar.gz cd meme-

      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.

      2. Configuring the installation

      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:

      ./configure parameters here

      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:

      ./configure

      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:

      ./configure --with-url="https://meme-suite.org/meme"

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

      ./configure --prefix=$HOME/memeyour install path --with-url="https://meme-suite.org/meme"

      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,

      ./configure --prefix=$HOME/memeyour install path --enable-build-libxml2 --enable-build-libxslt

      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,

      ./configure --prefix=$HOME/memeyour install path --with-url="http://"URL for MEME Suite on your web server --enable-web

      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:

      ./configure --prefix=$HOME/memeyour install path --with-url="http://"URL for MEME Suite on your web server --enable-web="https://meme-suite.org/meme/opal2/services"

      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 in the home directory to add the following lines:

      export CATALINA_BASE=<TOMCAT instance path> export CATALINA_HOME=<TOMCAT installation path>

      For most Tomcat installations the instance and the installation will be the same directory. Only if you have a multi-instance Tomcat installation will these be distinct directories.

      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 in CATALINA_BASE.

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

      ./configure --prefix=$HOME/memeyour install path --enable-web=Opal installation base URL --enable-webservice=path to Opal's deploy folder

      3. Building

      To build simply type while at the top directory:

      make

      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:

      make test

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

      4. Installing

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

      make install

      5. Setting PATH

      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, , , , , , etc., will be stored in the subdirectory of the installation. Supporting utilities are stored in the directory named (e.g., ) subdirectory. The steps to set your PATH will depend on the shell you use.

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

      export PATH=your install path/bin:your install path/libexec/meme-version #:$PATH

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

      setenv PATH your install path/bin:your install path/libexec/meme-version #:${PATH}

      [ Top ]


      Installing from a Mercurial repository

      The process of configuring, building, and installing MEME Suite from a Mercurial repository is the same as installing from a tarball, but with two extra, initial steps: you must check out the repository, and you must run the 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:

      hg clone ssh://[email protected]/tlbailey/meme

      Once you've checked out the source code you need to run the script:

      cd meme ./bootstrap

      The bootstrap script does a number of tasks like:

      • Checks the version of autoconf
      • Downloads the output example files and generates a file list for automake.
      • Uses ant to generate a file list of the website for automake.
      • Builds configure script.
      • Builds Makefile.in files from Makefile.am files.
      • Creates ARCHIVE_DATE and ARCHIVE_RELEASE files.

      You can now follow the configuration, building and install steps from installing from a tarball.

      [ Top ]


      Parallel MEME

      By default, 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 option.

      To compile the parallel version of MEME, 'configure' looks for , or . For running the parallel version of MEME, configure' looks on your PATH for MPI programs or .

      If your MPI is installed in non-standard place, use option when running 'configure' to specify the MPI installation directory.

      The parallel version of MEME is compiled and installed automatically via commands and .

      On some versions of Linux (e.g., Ubuntu), you may need to set the environment variable to zero to avoid an MPI warning message (about the point-to-point messaging module) when running MEME. You should initialize that variable in your shell. For example, if using the shell, add the following line to your shell configuration file in your home directory:

      export OMPI_MCA_btl_base_warn_component_unused=0

      Please see section Prerequisite software 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 superseded by OpenMPI, and is no longer under active development.

      [ Top ]


      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 :

      OptionNeeded forDefault value
      --prefix=​install pathProvide the installation location path.$HOME
      --enable-build-libxml2Forces MEME Suite to build and use libxml2 code included in MEME Suite distribution.disabled
      --enable-build-libxsltForces MEME Suite to build and use libxslt code included in MEME Suite distribution.disabled
      --enable-debugProduce an executable with debugging symbols.no debug
      --enable-optProduce an executable with optimization.compiler and OS dependent.
      --enable-serialProduce only serial version of MEME, do not build parallel version.disabled
      --enable-web=​opal services urlBuild web site applications. Must point it to MEME Suite web services exposed via Opal. Defaults to https://meme-suite.org/meme/opal2/services when the URL is not provided.disabled
      --enable-webservice=​opal deploy folderDeploy MEME Suite web services utilizing an existing Opal installation. The path to the deploy folder can be relative to CATALINA_BASE or absolute. If it is not specified than it is set to the folder in CATALINA_BASE.disabled
      --with-contact=​site administrator emailSet email of web site administrator.No site contact.
      --with-dev-contact=​developers emailSet email of developers.The current email address of the MEME Suite developers (given in configure.ac)
      --with-convert=​path to convert binarySet 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 directorySet path to databases.install path/db/
      --with-gs=​path to gs binarySet location of Ghostscript application.As found in PATH
      --with-logs=​logs directorySet path to logs.install path/LOGS/
      --with-drmaa-queue=​qsub commandSet the parameters for qsub for the DRMAA queue for normal jobs. The variables @[email protected] and @[email protected] should be used.
      Example: noble-meme-long.q -l [email protected]@,[email protected]@
      No DRMAA qsub command is given
      --with-drmaa-queue-short=​qsub commandSet the parameters for qsub for the DRMAA queue for short jobs. The variables @[email protected] and @[email protected] should be used.
      Example: noble-meme-short.q -l [email protected][email protected],[email protected][email protected]
      No DRMAA qsub command is given
      --with-maxtime=​max job timeSet wall time limit (sec) a normal web-submitted job may use.14400 (4 hours)
      --with-maxtime-short=​max job timeSet wall time limit (sec) a short web-submitted job may use.300 (5 minutes)
      --with-maxmemory=​max resident memorySet memory limit (GB) a normal web-submitted job may use.4 (4GB)
      --with-maxmemory-short=​max resident memorySet memory limit (GB) a short web-submitted job may use.1 (1GB)
      --with-streme-length-factor=​factorSet STREME input size limit per GB of max resident memory (see --with-maxmemory, above).1e6
      --with-mpidir=​mpi directorySet MPI installation path. See Parallel MEME section.Path of found mpicc
      --with-perl=​path to perl binarySet location of Perl interpreter.As found in PATH
      --with-python=​path to python binarySet location of Python interpreter.As found in PATH
      --with-source-url=​urlSet URL for the MEME SUITE source code and databases. Links to the source code and example input files in the website input forms, documentation, and in the output files generated by the MEME SUITE tools will point here.Default is the current location of the MEME SUITE source code and databases (given in configure.ac).
      --with-url=​urlSet URL for the MEME Suite web site. Links in the output HTML files and in the website input forms and documentation will point here.No URL is used.
      --with-alt-url=​urlSet URL for the alternate website for users to access if the main website is not operational.Default is there is no alternate website.
      --with-prev-url=​urlSet 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 numberSet 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=​urlSet URL for the GO term details page. The identifier will be substituted for GO_TERM_ID.http://amigo.geneontology.org/​cgi-bin/​amigo/​term_details?term=GO_TERM_ID
      --with-quota=​COUNT/TIMESet the quota limit for job submissions through the website as a COUNT of submissions during TIME seconds.No quota limits.
      --with-notices=​notices file nameSets the URL of the notices file relative to the top directory of the webapp.

      http://host/meme-/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, ) and specify 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., ). The notices file is written in the dialect of Markdown known as PageDown.
      The notices file is expected to be called and is in the top directory of the webapp.

      http://host/meme-/notices.txt

      --with-news=​news file nameSets the URL of the news file relative to the top directory of the webapp.

      http://host/meme-/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, ) and specify 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., ). The news file is written in the dialect of Markdown known as PageDown.
      The news file is expected to be called and is in the top directory of the webapp.

      http://host/meme-/news.txt

      --with-expiry=​days output retainedThis value should be set to the number of days that Opal retains a job after it has been submitted. Check the Opal configuration value in the file to determine how long Opal is set to retain data.The job expiry is set to 4 days.

      [ Top ]


      Installation Examples

      Example 1

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

      tar zxf meme-.tar.gz cd meme- ./configure --prefix=/opt/meme- make make test sudo make install

      Example 2

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

      tar zxf meme-.tar.gz cd meme- ./configure --prefix=/opt/meme- --with-url=https://meme-suite.org/meme make make test sudo make install

      Example 3

      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 in the form of a Java web archive ().

      The URL for the MEME web site will be 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.

      tar zxf meme-.tar.gz cd meme- ./configure \   --prefix=/opt/meme- \   --enable-web \   --with-url=http://host/meme- make make test make install

      Example 4

      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 in ).

      tar zxf meme-.tar.gz cd meme- ./configure \   --prefix=/opt/meme- \   --enable-web=http://host/opal2/services \   --enable-webservice \   --with-url=http://host/meme- make make test make install

      Example 5

      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.

      tar zxf meme-.tar.gz cd meme- ./configure \   --prefix=/opt/meme- \   --enable-web=http://host/opal2/services \   --enable-webservice \   --with-url=http://host/meme- \   --with-prev-url=http://host/meme_4.9.1 \   --with-prev-ver=4.9.1 \   --with-db=/opt/meme_db \   --with-notices=../notices.txt \   --with-news=../news.txt make make test make install

      [ Top ]


      Uninstalling

      You can uninstall MEME Suite by giving the command:

      make uninstall

      in the root of the build directory. This will remove all the files installed for the MEME Suite, but won't remove any directories that may have been created.

      [ Top ]


      Running regression tests

      There is a suit of tests that can be run to test MEME Suite output against known output. These tests can be run during the installation process. A quick "smoke test" can be run using the command:

      make test

      [ Top ]


      Installing sequence databases

      If you have installed MEME Suite web site and services then you can make it more useful by also installing sequence databases downloaded from FTP sites. The MEME Suite provides a tool for automatically downloading these databases and keeping them updated to the latest version.

      The most basic way of running the command simply specifies the location to store the databases.

      update-sequence-db your install path/db/fasta_databases

      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 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 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 option.

      update-sequence-db --csv path to databases/fasta_databases cp path to databases/fasta_databases/fasta_db.csv path to old distribution/etc/ cp path to databases/fasta_databases/fasta_db.index path to old install/etc/

      After the csv and index files are generated you need to move the index files to the folders of all your < 4.10.0 MEME Suite installs. Copying the csv is not strictly required but putting it in the folder of the distribution ensures that you don't accidentally overwrite the index file when doing a at a later date.

      If there are any database sources you don't want downloaded you can disable a source with the option.

      update-sequence-db --no_rsat path to databases/fasta_databases

      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 job that runs at regular intervals.

      After updating the databases you should restart the all the MEME Suite web applications.

      [ Top ]


      Installing motif databases

      Tomtom, MEME-ChIP, SpaMo, CentriMo and AME can make use of motif databases.

      1. Download the motif databases from here.
      2. Extract the databases from the gzipped tar:

        tar xzf motif_databases.X.tgz

        where "X" is the version number of the motif databases file
      3. Move the extracted databases folder:

        mv motif_databases path to databases/motif_databases

        Where the path to databases may just be the folder in the installation or another location if the 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 file to be copied into the distribution's directory and the rerunning of to generate and install the file.

      After updating the databases you should restart the all the MEME Suite web applications.

      [ Top ]


      Installing GOMO databases

      GOMO uses additional databases which need to be downloaded and installed.

      1. Download databases for GOMO from here.
      2. Extract the databases from the gzipped tar:

        tar xzf motif_databases.X.tgz

        where "X" is the version number of the GOMO databases file
      3. Move the extracted databases folder:

        mv gomo_databases path to databases/gomo_databases

        Where the path to databases may just be the folder in the installation or another location if the configure option was specified. On a split install this only needs to be done on the services install.
      4. In a split install copy the file to the etc folder of the website install.

      Note: releases prior to 4.10.0 require copying the file into the distribution's directory and rerunning to generate and install the file.

      After updating the databases you should restart the all the MEME Suite web applications.

      [ Top ]


      Reporting problems

      Make sure first that you really have a problem.

      Check your environment

      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?

      Look for the answers.

      Are you asking in the right place?

      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.

      Verify what you did.

      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.

      Report the problem.

      If all fails and you still have the problem, go ahead and send an email to [email protected]

      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 which is created by the configure script
      • if there are any errors or warnings output during the stage, attach created by the following commands (assuming bash shell):

        make clean make &> make.log

      • if any tests fail in the stage, attach created by the following command (assuming bash shell):

        make test &> test.log

      • if there are any errors or warnings output during the stage, attach created by the following command (assuming bash shell):

        make install &> install.log

      [ Top ]

      Sours: https://meme-suite.org/meme/doc/install.html

      Now meme install

      Reddit

      Reddit is the place where people come together to have the most authentic and interesting conversations on the internet—Where gaming communities, nostalgic internet forums, bloggers, meme-makers, and fandoms mingle alongside video streamers, support groups, news junkies, armchair experts, seasoned professionals, and artists and creators of all types.

      With over 100,000 communities about every topic you could think of (and a few you’d probably never think of if it wasn’t for the creativity of strangers on the internet), Reddit is the place where you can dive into anything and connect with people on any topic.

      A few things you’ll find on Reddit…

      ■ Thousands of communities
      Whether you're into breaking news, sports, TV fan theories, or a never-ending stream of the internet's cutest animals, there's a community on Reddit for you.
      ■ Laughs, lols, and plenty of ridiculousness
      Lose track of vast amounts of time as you find memes, bananas for scale, bread stapled to trees, cat videos, and more of the absurd and oddly absorbing.
      ■ Discussions that will draw you in
      The real action is always in the comments. Reddit’s discussion threads are where community members jump in to provide commentary, humor, and insight.
      ■ Answers to questions you’re too afraid to ask in public
      Recipes, street fashion, career help, fitness plans, and more—find ideas and inspiration for whatever you want to do.
      ■ Live video streams, chats, and talks
      Want to know what people are doing right now? Streaming videos, live chats, and live audio conversations give you a variety of ways to connect with people in the moment.
      ■ Crowd-sourced points of view on just about everything
      Product reviewers, music critics, sports fans, or doge enthusiasts—find people that obsess and care about whatever it is you’re interested in.
      ■ Anonymous profiles so you can do you
      On Reddit, you (not your job, number of friends, or social status) define who you are.
      ■ Lots and lots of cats

      Reddit Premium:
      Purchase Reddit Premium and enjoy an ads-free experience, 700 coins for every month you’re subscribed, and access to premium avatar gear, r/lounge, custom app icons, and more.

      Payment will be charged on a recurring monthly or annual basis to your Google Play account. Your monthly or annual Premium subscription will automatically renew unless you cancel at least 24 hours before your subscription ends. Cancel anytime in your device’s Account Settings. No partial refunds.

      Privacy Policy: https://www.redditinc.com/policies/privacy-policy
      User Agreement: https://www.redditinc.com/policies/user-agreement
      Content Policy: https://www.redditinc.com/policies/content-policy

      Download the official Reddit app today.

      Sours: https://play.google.com/
      If Squid Game were a Try Not To Laugh 299

      Poster Now - Meme Creator for Android


      • Release date: 2021-09-24
      • Current version: 3.3.6
      • File size: 47.39 MB
      • Developer: Photo & Video Labs
      • Compatibility: Requires iOS 9.0 or later. or Android KitKat 4.4, Lollipop 5.0, Marshmallow 6.0, Nougat 7.0, Oreo 8.0, Android Pie 9.0, versions 10, 11, 12 or later

      * Create unique POSTERS, MEMES and collages! * Be creative and have real fun with your friends! * Use various backgrounds, STICKERS and mottos! This app provides you with a great number of handy templates for funny collages. Feel free to create posters of any kind. Add your own photo as a background, choose a picture from your gallery or use a standard background. Write your text and select any stickers you like. Don't forget to share your memes with friends! With this new photo editor you have a great chance to show your creativity and create posters suitable for all occasions!


      Apk Mirror 1: : Download APK



      Sours: https://baixarapk.gratis/en/app/1031187801/make-a-poster-meme-creator

      You will also like:

      The MEME Suite

      Motif-based sequence analysis tools

      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 SOAP services. The SOAP services are provided through Tomcat and Opal, 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:


      Quick Install (for Linux, OS X and Cygwin systems)

      1. Type the following commands

        tar zxf meme_.tar.gz cd meme_ ./configure --prefix=$HOME/meme --with-url=http://meme-suite.org --enable-build-libxml2 --enable-build-libxslt make make test make install

      2. Edit your shell configuration file to add to your shell's path. This can often be done by editing the file named to add the following line:

        export PATH=$HOME/meme/bin:$PATH

      Notes:

      • This installs only the command-line versions of programs. Refer to Installing from a tarball 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 http://meme-suite.org for additional processing when clicked. Refer to the Installing from a tarball if you do not want this feature.
      • The 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 Prerequisite software installed. You will want to read that section of this manual and run the script as described there to see what you may be missing.

      [ Top ]


      Prerequisite software

      Most of the software mentioned here is standard on many UNIX-like systems. To build MEME Suite with just the command-line tools you will need:

      Optional software includes:

      Additionally if you want to install MEME Suite web server you will also need:

      Perl (version 5.16 or higher)

      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 directory of the MEME Suite installation files.

      cd scripts perl dependencies.pl

      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:

      Checking Required Perl Modules: Math::CDF missing. 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.

      sudo cpan Math::CDF

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

      sudo apt-get install libexpat1-dev

      Python (version 2.7.x or 3.x)

      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.

      zlib

      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:

      sudo port install zlib

      On Ubuntu and related distributions it can be installed with the command:

      sudo apt-get install zlib1g-dev

      Assorted Common Utilities

      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:

      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:

      sudo port install autoconf sudo port install automake sudo port install libtool

      Ubuntu and related distributions can use the install commands:

      sudo apt-get install autoconf sudo apt-get install automake sudo apt-get install libtool

      Installing command-line tools on OS X

      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.

      MacPorts on OS X [optional]

      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

      port list 'tomcat*'

      and MacPorts will tell you if it can install the package.

      Ghostscript [optional]

      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 avaliable.

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

      sudo port install ghostscript

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

      MPI [recommended]

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

      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:

      sudo port install openmpi

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

      sudo port select --set mpi openmpi-mp-fortran

      libxml2 (version 2.6.0 or later), libxslt (version 1.1 or later) & libexslt [optional]

      The MEME Suite includes the code for libxml2, libxslt and the extensions in libexslt 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]

      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:

      sudo apt-get install default-jdk

      Apache Ant [for web server or developer only]

      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 script is run.

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

      sudo port install apache-ant

      Ubuntu and related distributions can use the install command:

      sudo apt-get install ant

      Apache Tomcat (version 7 or higher) [for web server only]

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

      Opal (version 2.5) [for web server only]

      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.

      Batch Scheduler [for web server on a compute cluster]

      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:

      [ Top ]


      Getting the source

      Releases of the MEME Suite are available from http://meme-suite.org/doc/download.html/ (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.

      [ Top ]


      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 http://meme-suite.org/doc/download.html/ (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:

      cd meme_ patch -p1 -i ../PATH_TO_PATCH/patch__1 make make test make install

      If you have more than one patch to install simply group all the patch commands together and only run the make commands once.

      Some patches will require "-p0" to be passed as an argument instead of "-p1" but the readme will specify which to use.

      [ Top ]


      MEME Suite Directories

      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 which contains the motif databases, a folder which contains the gomo databases and a folder 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 in the directory and the SQLite library in the directory .

      [ Top ]


      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 Installing from an Mecurial repository.

      Four steps are required to install the MEME Suite from a distribution tarball:

      1. Unzip and untar the distribution
      2. Configure the installation using the command.
      3. Build MEME Suite using the command
      4. Test the MEME Suite build by using the command.
      5. Install MEME Suite using the command.

      1. Unzip and untar the distribution:

      For example for release you should use the commands:

      tar zxf meme_.tar.gz cd meme_

      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.

      2. Configuring the installation

      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:

      ./configure parameters here

      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:

      ./configure

      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 meme-suite.org, the simplest configuration command is:

      ./configure --with-url="http://meme-suite.org"

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

      ./configure --prefix=$HOME/memeyour install path --with-url="http://meme-suite.org"

      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 meme-suite.org. 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 parameters. For example,

      ./configure --prefix=$HOME/memeyour install path --enable-build-libxml2 --enable-build-libxslt

      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 http://meme-suite.org/opal2/services. For example,

      ./configure --prefix=$HOME/memeyour install path --with-url="http://"URL for MEME Suite on your web server --enable-web

      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 http://meme-suite.org/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 meme-suite.org server:

      ./configure --prefix=$HOME/memeyour install path --with-url="http://"URL for MEME Suite on your web server --enable-web="http://meme-suite.org/opal2/services"

      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_HOME to the path to the root directory of Tomcat. This can often be done by editing the file named to add the following line:

      export CATALINA_HOME=/opt/apache-tomcatTOMCAT path

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

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

      ./configure --prefix=$HOME/memeyour install path --enable-web=Opal installation base URL --enable-webservice=path to Opal's deploy folder

      3. Building

      To build simply type while at the top directory:

      make

      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:

      make test

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

      4. Installing

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

      make install

      5. Setting PATH

      To use the MEME Suite on the command-line you should set the environment variable PATH so your shell can find the newly installed tools. The steps will depend on the shell you use.

      For the common Bourne-again shell (aka bash) you should edit the file called in your home directory to add the following line:

      export PATH=your install path/bin:$PATH

      For C shell (aka csh and the similar tcsh) you should edit the file called in your home directory to add the following line:

      setenv PATH your install path/bin:${PATH}

      [ Top ]


      Installing from a Mercurial repository

      The process of configuring, building, and installing MEME Suite from a Mercurial repository is the same as installing from a tarball, but with two extra, initial steps: you must check out the repository, and you must run the 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:

      hg clone ssh://[email protected]/tlbailey/meme

      Once you've checked out the source code you need to run the script:

      cd meme ./bootstrap

      The bootstrap script does a number of tasks like:

      • Checks the version of autoconf
      • Downloads the output example files and generates a file list for automake.
      • Uses ant to generate a file list of the website for automake.
      • Builds configure script.
      • Builds Makefile.in files from Makefile.am files.
      • Creates ARCHIVE_DATE and ARCHIVE_RELEASE files.

      You can now follow the configuration, building and install steps from installing from a tarball.

      [ Top ]


      Parallel MEME

      By default, 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 option.

      To compile the parallel version of MEME, 'configure' looks for , or . For running the parallel version of MEME, configure' looks on your PATH for MPI programs or .

      If your MPI is installed in non-standard place, use option when running 'configure' to specify the MPI installation directory.

      The parallel version of MEME is compiled and installed automatically via commands and .

      Please see section Prerequisite software 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.

      [ Top ]


      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 :

      OptionNeeded forDefault value
      --prefix=​install pathProvide the installation location path.$HOME
      --enable-build-libxml2Forces MEME Suite to build and use libxml2 code included in MEME Suite distribution.disabled
      --enable-build-libxsltForces MEME Suite to build and use libxslt code included in MEME Suite distribution.disabled
      --enable-debugProduce an executable with debugging symbols.no debug
      --enable-optProduce an executable with optimization.compiler and OS dependent.
      --enable-serialProduce only serial version of MEME, do not build parallel version.disabled
      --enable-web=​opal services urlBuild web site applications. Must point it to MEME Suite web services exposed via Opal. Defaults to http://meme-suite.org/opal2/services when the URL is not provided.disabled
      --enable-webservice=​opal deploy folderDeploy MEME Suite web services utilizing an existing Opal installation. The path to the deploy folder can be relative to CATALINA_HOME or absolute. If it is not specified than it is set to the folder in CATALINA_HOME.disabled
      --with-contact=​site administrator emailSet email of web site administrator.No site contact.
      --with-dev-contact=​developers emailSet email of developers.[email protected]
      --with-convert=​path to convert binarySet 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 directorySet path to databases.install path/db/
      --with-gs=​path to gs binarySet location of Ghostscript application.As found in PATH
      --with-logs=​logs directorySet path to logs.install path/LOGS/
      --with-maxtime=​max job timeSet wall time limit (sec) a web-submitted job started by the web server may use.18000 (5 hours)
      --with-mpidir=​mpi directorySet MPI installation path. See Parallel MEME section.Path of found mpicc
      --with-perl=​path to perl binarySet location of Perl interpreter.As found in PATH
      --with-python=​path to python binarySet location of Python interpreter.As found in PATH
      --with-url=​urlSet URL for the MEME Suite web site used by buttons on the output of MEME Suite tools.No URL is used.
      --with-prev-url=​urlSet 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 numberSet 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=​urlSet URL for the GO term details page. The identifier will be substituted for GO_TERM_ID.http://amigo.geneontology.org/​cgi-bin/​amigo/​term_details?term=GO_TERM_ID
      --with-quota=​COUNT/TIMESet the quota limit for job submissions through the website as a COUNT of submissions during TIME seconds.No quota limits.
      --with-notices=​notices file nameSets the URL of the notices file relative to the top directory of the webapp.

      http://host/meme_/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, ) and specify 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., ). The notices file is written in the dialect of Markdown known as PageDown.
      The notices file is expected to be called and is in the top directory of the webapp.

      http://host/meme_/notices.txt

      --with-news=​news file nameSets the URL of the news file relative to the top directory of the webapp.

      http://host/meme_/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, ) and specify 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., ). The news file is written in the dialect of Markdown known as PageDown.
      The news file is expected to be called and is in the top directory of the webapp.

      http://host/meme_/news.txt

      --with-expiry=​days output retainedThis value should be set to the number of days that Opal retains a job after it has been submitted. Check the Opal configuration value in the file to determine how long Opal is set to retain data.The job expiry is set to 4 days.

      [ Top ]


      Installation Examples

      Example 1

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

      tar zxf meme_.tar.gz cd meme_ ./configure --prefix=/opt/meme_ make make test sudo make install

      Example 2

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

      tar zxf meme_.tar.gz cd meme_ ./configure --prefix=/opt/meme_ --with-url=http://meme-suite.org make make test sudo make install

      Example 3

      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 in the form of a Java web archive ().

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

      tar zxf meme_.tar.gz cd meme_ ./configure \   --prefix=/opt/meme_ \   --enable-web \   --with-url=http://host/meme_ make make test make install

      Example 4

      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 in ).

      tar zxf meme_.tar.gz cd meme_ ./configure \   --prefix=/opt/meme_ \   --enable-web=http://host/opal2/services \   --enable-webservice \   --with-url=http://host/meme_ make make test make install

      Example 5

      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.

      tar zxf meme_.tar.gz cd meme_ ./configure \   --prefix=/opt/meme_ \   --enable-web=http://host/opal2/services \   --enable-webservice \   --with-url=http://host/meme_ \   --with-prev-url=http://host/meme_4.9.1 \   --with-prev-ver=4.9.1 \   --with-db=/opt/meme_db \   --with-notices=../notices.txt \   --with-news=../news.txt make make test make install

      [ Top ]


      Uninstalling

      You can unistall MEME Suite by giving the command:

      make uninstall

      in the root of the build directory. This will remove all the files installed for the MEME Suite, but won't remove any directories that may have been created.

      [ Top ]


      Running regression tests

      There is a suit of tests that can be run to test MEME Suite output against known output. These tests can be run during the installation process. A quick "smoke test" can be run using the command:

      make test

      [ Top ]


      Installing sequence databases

      If you have installed MEME Suite web site and services then you can make it more useful by also installing sequence databases downloaded from FTP sites. The MEME Suite provides a tool for automatically downloading these databases and keeping them updated to the latest version.

      The most basic way of running the command simply specifies the location to store the databases.

      update-sequence-db your install path/db/fasta_databases

      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 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 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 option.

      update-sequence-db --csv path to databases/fasta_databases cp path to databases/fasta_databases/fasta_db.csv path to old distribution/etc/ cp path to databases/fasta_databases/fasta_db.index path to old install/etc/

      After the csv and index files are generated you need to move the index files to the folders of all your < 4.10.0 MEME Suite installs. Copying the csv is not strictly required but putting it in the folder of the distribution ensures that you don't accidently overwrite the index file when doing a at a later date.

      If there are any database sources you don't want downloaded you can disable a source with the option.

      update-sequence-db --no_rsat path to databases/fasta_databases

      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 job that runs at regular intervals.

      After updating the databases you should restart the all the MEME Suite web applications.

      [ Top ]


      Installing motif databases

      Tomtom, MEME-ChIP, SpaMo, CentriMo and AME can make use of motif databases.

      1. Download the motif databases from here.
      2. Extract the databases from the gziped tar:

        tar xzf motif_databases.X.tgz

        where "X" is the version number of the motif databases file
      3. Move the extracted databases folder:

        mv motif_databases path to databases/motif_databases

        Where the path to databases may just be the folder in the installation or another location if the 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 file to be copied into the distribution's directory and the rerunning of to generate and install the file.

      After updating the databases you should restart the all the MEME Suite web applications.

      [ Top ]


      Installing GOMO databases

      GOMO uses additional databases which need to be downloaded and installed.

      1. Download databases for GOMO from here.
      2. Extract the databases from the gziped tar:

        tar xzf motif_databases.X.tgz

        where "X" is the version number of the GOMO databases file
      3. Move the extracted databases folder:

        mv gomo_databases path to databases/gomo_databases

        Where the path to databases may just be the folder in the installation or another location if the configure option was specified. On a split install this only needs to be done on the services install.
      4. In a split install copy the file to the etc folder of the website install.

      Note: releases prior to 4.10.0 require copying the file into the distribution's directory and rerunning to generate and install the file.

      After updating the databases you should restart the all the MEME Suite web applications.

      [ Top ]


      Reporting problems

      Make sure first that you really have a problem.

      Check your environment

      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?

      Look for the answers.

      Are you asking in the right place?

      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.

      Verify what you did.

      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.

      Report the problem.

      If all fails and you still have the problem, go ahead and send an email to [email protected] 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 which is created by the configure script
      • if there are any errors or warnings output during the stage, attach created by the following commands (assuming bash shell):

        make clean make &> make.log

      • if any tests fail in the stage, attach created by the following command (assuming bash shell):

        make test &> test.log

      • if there are any errors or warnings output during the stage, attach created by the following command (assuming bash shell):

        make install &> install.log

      [ Top ]

      Sours: http://web.mit.edu/meme_v4.11.4/share/doc/install.html


      3664 3665 3666 3667 3668