root/INSTALL

***Installation Documentation***

How to Install Standard MAKER

Note:  When using Mac OS-X and installing MAKER you must either be a system
administrator with sudo privleges or be logged in as root on the terminal for
some parts of the installation.


1.  You need to have perl 5.8.0 or higher installed.  You can verify this by
    typing perl -v on the command line in a terminal.


2.  Install BioPerl 1.6 or higher.  Download the Core Package from
    http://www.bioperl.org

  -quick and dirty installation-
  (with this option, not all of bioperl will work, but what MAKER uses will)

  a.  Download and unpack the most recent BioPerl package to a directory of your
      choice, or use Subversion to get the most current version of BioPerl. See
      http://www.bioperl.org for details on how to download using Subversion.
      You will then need to set PERL5LIB in your .bash_profile to the location
      of bioperl (i.e. export PERL5LIB="/usr/local/bioperl-live:$PERL5LIB").

  -full BioPerl instalation-
  (you will need sudo privileges, root access, or CPAN configured for local
   installation to continue with this option)

  a.  Type perl -MCPAN -e shell into the command line to set up CPAN on your
      computer before installing bioperl (CPAN helps install perl dependencies
      needed to run bioperl).  For the most part just accept any default options
      by hitting enter during setup.
  b.  Type install Bundle::CPAN on the cpan command line.  Once again just press
      enter to accept default installation options.
  c.  Type install Module::Build on the cpan command line.  Once again just
      press enter to accept default installation options.
  d.  Type install Bundle::BioPerl on the cpan command line.  Once again press
      enter to accept default installation options.
  e.  Unpack the downloaded bioperl tar file to the directory of your choice or
      use Subversion to get the most up to date version.  Then use the terminal
      to find the directory and type perl Build.PL in the command line, then
      type ./Build test, then if all tests pass, type ./Build install.  This
      will install BioPerl where perl is installed.  Press enter to accept all
      defaults. For Mac OS-X BioPerl will install to /Library/Perl/5.8.6/.


3.  Install WuBlast 2.0 or higher
    (WuBlast has become AB-Blast and is no longer freely available, so if you
    are not lucky enough to have an existing copy of WuBlast, you can use NCBI
    BLAST instead.  See NCBI BLAST documentation for installation instructions.
    It is important to note that WuBlast is a prerequisite for RepeatMasker
    installation, so if you do not have WuBlast, then you will have to install
    Cross_match to get RepeatMasker to work.  See RepeatMasker documentation.)

  a.  Unpack the tar file into the directory of your choice (i.e. /usr/local).
  b.  Add the following in your .bash_profile (value depend on where you chose
      to install wublast):
                export WUBLASTFILTER="/usr/local/wublast/filter"
                export WUBLASTMAT="/usr/local/wublast/matrix"
  c.  Add the location where you installed WuBlast to your PATH variable in 
      .bash_profile (i.e. PATH="/usr/local/wublast:$PATH").


4.  Install SNAP.  Download from http://homepage.mac.com/iankorf/

  a.  Unpack the SNAP tar file into the directory of your choice (ie /usr/local)
  b.  Add the following to your .bash_profile file (value depends on where you
      choose to install snap):  export ZOE="/usr/local/snap/Zoe"
  c.  Navigate to the directory where snap was unpacked (i.e. /usr/local/snap)
      and type make
  d.  Add the location where you installed SNAP to your PATH variable in
      .bash_profile (i.e. export PATH="/usr/local/snap:$PATH").


5.  Install RepeatMasker. Download from http://www.repeatmasker.org

  a.  The most current version of RepeatMasker requires a program called TRF.
      This can be downloaded from http://tandem.bu.edu/trf/trf.html
  b.  The TRF download will contain a single executable file.  You will need to
      rename the file from whatever it is to just 'trf' (all lower case).
  c.  Make TRF executable by typing chmod +x+u trf.  You can then move this file
      wherever you want.  I just put it in the /RepeatMasker directory.
  d.  Unpack RepeatMasker to the directory of your choice (i.e. /usr/local).
  e.  Now in the RepeatMasker directory type perl ./configure in the command
      line. You will be asked to identify the location of perl, wublast, and
      trf.  The script expects the paths to the folders containing the
      executables (because you are pointing to a folder the path must end in a 
      '/' character or the configuration script throws a fit).
  f.  Add the location where you installed RepeatMasker to your PATH variable in
      .bash_profile (i.e. export PATH="/usr/local/RepeatMasker:$PATH").
  g.  You must register at http://www.girinst.org and download the Repbase
      repeat database, Repeat Masker edition, for RepeatMasker to work.
  h.  Unpack the contents of the RepBase tarball into the RepeatMasker/Libraries
      directory.


6.  Install Exonerate 1.4 or higher.  Download from
    http://www.ebi.ac.uk/~guy/exonerate

  a.  Exonerate has pre-comiled binaries for many systems; however; for Mac OS-X
      you will have to download the source code and complile it yourself by
      following steps b though d.
  b.  You need to have Glib and Glib 2.0 installed.  The easiest way to do this
      is to install fink and then type fink install glib and fink install
      glib2-dev.
  c.  Change to the directory containing the Exonerate package to be compiled.
  d.  To install exonerate in the directory /usr/local/exonerate, type:
      ./configure -prefix=/usr/local/exonerate -> then type make -> then type
      make install
  e.  Add the location where you installed exonerate to your PATH variable in
      .bash_profile (i.e. export PATH="/usr/local/exonerate/bin:$PATH").


7.  Install MAKER.  Download from http://www.yandell-lab.org

  a.  Unpack the MAKER tar file into the directory of your choice (i.e.
      /usr/local).
  b.  Change to the directory maker/perl and run Install.PL by typing:
      perl Install.PL
  c.  Now add the following to your .bash_profile if you haven't already:
        export WUBLASTFILTER="where_wublast_is/filter"
        export WUBLASTMAT="where_wublast_is/matrix"
        export ZOE="where_snap_is/Zoe"
        export AUGUSTUS_CONFIG_PATH="where_augustus_is/config
  d.  Add the location where you installed MAKER to your PATH variable in
      .bash_profile (i.e. export PATH=/usr/local/maker/bin:$PATH).
  e.  You can now run a test of MAKER by following the instructions in the MAKER
      README file.


See the README file for details on installing mpi_maker


(OPTIONAL COMPONENTS)

1. Augustus 2.0 or higher.  Download from http://augustus.gobics.de

  a.  Change to the directory containing the Augustus package to be compiled.
  b.  Unpack Augustus to the directory of your choice (i.e. /usr/local).
  c.  Change to the src/ directory inside the extracted augustus folder.
  d.  Install and compile Augustus by typing: make
  e.  Add the following to your .bash_profile file (value depends on where you
      install augutus):  export AUGUSTUS_CONFIG_PATH=/usr/local/augustus/config
  f.  Add the location where you installed augustus to your PATH variable in
      .bash_profile (i.e. export PATH=/usr/local/augustus/bin:$PATH).


2. GeneMark-ES.  Download from http://exon.biology.gatech.edu

  a.  See installation documentation.

3. FGENESH 2.4 or higher.  Purchase from http://www.softberry.com

  a.  See installation documentation.

4. GeneMarkS.  Used for prokaryotic genomes only.
   Download from http://exon.biology.gatech.edu

  a.  See installation documentation.