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Installation notes for MEME version 4.11.1 - Jan. 7, 2016

This installs only the command-line versions of programs

Home Page

Prerequisites

Installation

  1. $ ver="4.11.1";patchver="$ver";mver="12.12";gver="3.2"
  2. $ cd /programinstallers/
  3. Download MEME Suite
    $ wget -N http://meme-suite.org/meme-software/$ver/meme_$patchver.tar.gz
  4. Download motif databases
    $ wget -N http://meme-suite.org/meme-software/Databases/motifs/motif_databases.$mver.tgz
  5. Download gomo databases
    $ wget -N http://meme-suite.org/meme-software/Databases/gomo/gomo_databases.$gver.tgz
  6. Uncompress
    $ tar -zxvf meme_$patchver.tar.gz
  7. $ tar -zxvf motif_databases.$mver.tgz
  8. $ tar -zxvf gomo_databases.$gver.tgz
  9. Compile
    $ cd meme_$ver
  10. $ mkdir /usr/local/bin/meme
  11. $ cp -pv ../motif_databases/motif_db.csv ../gomo_databases/gomo_db.csv etc/ 
    `../motif_databases/motif_db.csv' -> `etc/motif_db.csv'
`../gomo_databases/gomo_db.csv' -> `etc/gomo_db.csv'
  12. $ perl scripts/dependencies.pl 
    Checking Required Perl Modules:
XML::Compile::SOAP11 missing. Used for downloading sequence databases from RSAT
XML::Compile::WSDL11 missing. Used for downloading sequence databases from RSAT
XML::Compile::Transport::SOAPHTTP missing. Used for downloading sequence databases from RSAT

Checking Optional Modules:
Log::Log4perl missing. Used for logging and debugging by developers.
  13. $ ./configure --prefix=/usr/local/bin/meme --with-url="http://meme-suite.org" --enable-build-libxml2 --enable-build-libxslt
    … 
            ========================
        Configuration parameters
        ========================

  Install path:               /usr/local/bin/meme
  Install UID:                
  Version:                    4.11.1
  C compiler:                 gcc
  C compiler flags:           -std=gnu89 -Wall -Wno-unused -DUNIX -D__USE_FIXED_PROTOTYPES__   -O3
  Linker:                     /usr/bin/ld -m elf_x86_64
  Special Libs:               -lmpi -lz -lm 
  MPICC                       /usr/bin/mpicc
  MPIRUN                      /usr/bin/mpirun
  MPI_CMD                     /usr/bin/mpirun -np
  MPIINC                      -DMPI -I/usr/include
  MPILIBDIR                   /usr/lib
  MPIFLAGS                    -DPARALLEL 
  MEME URL:                   http://meme-suite.org
  PREVIOUS VERSION URL:       
  SERVER CONTACT:             
  DEVELOPER CONTACT:          meme-suite@uw.edu
  GO-SERVER URL:              http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO_TERM_ID
  PERL:                       /usr/local/bin/perl
  PYTHON:                     /usr/bin/python
  CONVERT:                    /usr/bin/convert
  GHOSTSCRIPT:                /usr/bin/gs
  BUILD LIBXML2:              yes
  LIBXML2 compiler flags:     -I${top_srcdir}/src/libxml2/include
  LIBXML2 libs:               ${top_builddir}/src/libxml2/libxml2.la
  BUILD LIBXSLT:              yes
  LIBXSLT compiler flags:     -I${top_srcdir}/src/
  LIBXSLT libs:               ${top_builddir}/src/libxslt/libxslt.la
  MEME DB:                    ${prefix}/db
  MEME LOGS:                  ${prefix}/LOGS
  MEME TEMP FILES:            
  OPAL URL:                   no
  OPAL DEPLOY DIRECTORY:      

  Run the following commands to compile, test and install meme:
        make
        make test
        make install
  14. $ make
  15. $ make test (takes a long time)
    … 
    ============================================================================
Testsuite summary for meme 4.11.1
============================================================================
# TOTAL: 99
# PASS:  99
# SKIP:  0
# XFAIL: 0
# FAIL:  0
# XPASS: 0
# ERROR: 0
============================================================================
    …
  16. $ sudo make install
  17. $ cd ..
  18. Move databases to installed location
    $ sudo mv motif_databases gomo_databases /usr/local/bin/meme/db/
  19. Add to the default PATH
    $ sudo nano /etc/profile
    …
    PATH="$PATH:/usr/local/bin/meme/bin"
    …
  20. Cleanup
    $ rm meme_$ver -rf