Installing MEME from RPMs

Prerequisite software

The RPMS are build on a the machine that has the following software installed that will be required during runnign MEME:

Perl (v.5.6.1 or higher). See http://www.perl.org for download and installation instructions.
The CGI.pm perl module.
For a parallel version of MEME, an LAM MPI implementation and SGE batch scheduler :
- LAM from http://www.lam-mpi.org The LAM installation is expeted in /opt/lam/gnu. The binary meme_p depends on the shareed libraries:
  - /opt/lam/gnu/lib/liblamf77mpi.so.0
  - /opt/lam/gnu/lib/libmpi.so.0
  - /opt/lam/gnu/lib/liblam.so.0
- SGE from http://gridengine.sunsource.net. SGE can be installed anywhere, and the SGE-install-dir/bin must be included in users PATH.

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Getting the RPMs

Currently, RPMs for MEME version 3.5.2 are provided for i386 and x86_64 architectures (Linux CentOS) and are available from http://meme.nbcr.net/downloads/.

The RPMs are distributed as a tarball meme_3.5.2.ARCH.rpm.tar.gz which contains needed RPMS, and the script the must be run after the installation of RPMs (the script provides additional required setup).

When downloading the software, please make sure you verify the corresponding checksum. Here is the checksum information for available MEME RPM tarballs:

File	md5sum
meme_3.5.2.i386.rpm.tar.gz	9ba0dafa96407024ea5469f4959b07fb
meme_3.5.2.x86_64.rpm.tar.gz	ae9bc68588e29bb30d7ea4dc59fdb477

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Installing RPMs

All the commands below must be run as a superuser.

1. Create user meme prior to installation:

$ /usr/sbin/useradd -c "Meme user " -d /export/home/meme meme

Use command and path that is appropriate for your system.

1. Unzip and untar the distribution:

$ gunzip -c meme_3.5.2.ARCH.rpm.tar.gz | tar xvf -

1. Install RPMSs

$ rpm -i meme-3.5.2-0.ARCH.rpm
$ rpm -i meme-db-3.5.2-0.ARCH.rpm
$ rpm -i -force meme-web-3.5.2-0.ARCH.rpm

2. Run postinstall script

Take a look at the postinstall script postinstall-meme.sh to see what commands will be executed and what changes will be done to your system. At the top, there is a section where some variables are set. Make needed changes if any, then execute:
$ ./postinstall-meme.sh

3. Starting servers

The servers should be started as user meme

To start servers, execute:
$ /etc/init.d/rocks-meme start

To check server status, execute:
$ /opt/meme/bin/memed status

To stop servers, execute:
$ /etc/init.d/rocks-meme stop

The servers will be automatically started upon reboot.

4. Installing mast databases
Only some databases are probided, the rest will need to be downloaded on a regular basis. The tools for download are included. Here is the list of the ocmmands that can be executed at the desired frequencey (daily or weekly):

$ cd /opt/meme/db

$ . /opt/meme/etc/meme.sh

$ update_mast_databases yourmail@your.address `pwd` < /opt/meme/etc/mast_db.list

The resulting files in the databases directory will be around 26Gb. If your /opt/meme/db directory does not have anough space create a database directory on a filesystem with the sufficient space and make a link to /opt/meme/db. It can take time to download all the databases, and the connections to some sites from which files are downloaded may be not always available. The result of the download will be emailed to the address specified by yourmail@your.address. If there are errors, they will be noted in the email, and the command to install the databases will need to be repeated.

5. Configuring apache web access

The HTTP DocumentRoot is assumed to be /var/www/html, and a link is created during postinstall step. The URL for web access is http://your.host.name/meme/. Modify postinstall-meme.sh if your system requires different HTTP settings.

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Resulting installation files

Installing RPMs will provide for installing MEME servers and clients, including the web services, and the following directory structure will be created in /opt/meme:

    bin/    db/    etc/    lib/    tests/    web/

In addition, a postinstall-meem.sh creates

    /home/meme/LOGS

Directories contents:

bin/

MEME and MAST executables and scripts

db/

this directory is initially partially filled with the database files, and needs to be updated (run update_mast_databases command.

etc/

contains the following files

mast_db.list - databases list, for running update_mast_databases command
mast.doc, meme.doc - text files used by a few commands to provide usage info
meme_config - localization file, holds the variables needed for running scripts
prior1.plib, prior30.plib - these files are used by MEME
meme.csh - for setting user environment for tcsh or csh
meme.sh - for setting user environment for sh or bash

lib/

contains common Perl modules

LOGS/

directory for temporary files created by mast or MEME when jobs are submitted via web

tests/

known correct output of MEME and MAST for specific sequences and databases. These files are used when running make test during installation or bin/runtests

web/

contains files necessary to setup up a web-based access to MEME/MAST servers.

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Using meme/mast

Before using MEME and MAST, users must add a few environment variables. All needed variables are defined in meme.csh and meme.sh files.

If using csh or tcsh, execute the following command:
$ source install-path/etc/meme.csh
To make the addition of these variables automatic upon login, add a line to your .cshrc or .tcshrc file:
$ source install-path/etc/meme.csh
If using sh or bash, execute the following command:
$ . install-path/etc/meme.sh
To make the addition of these variables automatic add a line to your .profile or .bash_profile file:
$ . install-path/etc/meme.sh

The install-path should be a full path to the installation directory. To find out how to use MEME or MAST execute respectively:
$ meme
$ mast

Both commands print usage on stdout.

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Running regression tests

There is a suit of tests that can be run to test MEME and MAST output against known output. These tests can be run at any time after the installation of newly compiled MEME and MAST binaries (meme.bin and mast.bin). These tests can take a long time. The output files from the tests go into the newly created directory install-path/tests/results/. 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 install-path/tests/. To run the regression tests do:

$ install-path/bin/runtests

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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 file 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 meme@nbcr.net. 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, ...
- Describe the exact problem symptoms, and whether they are reproducible. Provide the relevant output from running your commands that indicates what the error was.

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