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# Copyright Georgia Institute of Technology, Atlanta, Georgia, USA
# Distributed by GeneProbe Inc., Atlanta, Georgia, USA
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Installation instructions for GeneMark* software

a. Copy the content of distribution to desired location.
b. Install the key: copy key "gm_key" into users home directory as:

  gunzip gm_key.gz

  cp gm_key ~/.gm_key

Program is ready for execution.

Perl scripts are configured with default Perl location at "/usr/bin/perl".
Default path to Perl can be changed by script "perl change_path_in_perl_scripts.pl" 
from GeneMark* distribution folder.

The following Perl modules are required:
   YAML
   Hash::Merge
   Parallel::ForkManager
   MCE::Mutex
   Thread::Queue
   threads
   Math::Utils

Perl libraries should be at minimum:

MCE to version 1.8
Parallel::ForkManager to version 2
Thread::Queue version 3

To get the Perl library versions run:

perl -MMCE -e 'print $MCE::VERSION ."\n";'
perl -MParallel::ForkManager -e 'print $Parallel::ForkManager::VERSION ."\n";'
perl -MThread::Queue -e 'print $Thread::Queue::VERSION ."\n";'

If some of the Perl modules are missing, then modules can be installed from CPAN 
or other method available on your platform.

For example:
  see https://www.cpan.org/modules/INSTALL.html
  cpan App::cpanminus
  cpanm YAML
or
  AWS or RedHat
  yum search YAML
  yum install YAML*  # replace with full name from search
or
  UBUNTU
  apt search YAML
  apt install YAML*  # replace with full name from search

Code was tested on Perl 5.10 or higher.
Python 3.3 or higher is required for GeneMark-EP run mode.

To check completeness of installation, run script "check_install.bash"

To verify that the entire software is working correctly, 
run a test example in GeneMark-E-tests folder.

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