INSTALL

# GeneMark-ETP project  

## GENERAL INSTALLATION ------------  
Download GeneMark-ETP project from GitHub:  
   https://github.com/gatech-genemark/GeneMark-ETP  

Files required for GeneMark-ETP execution are in the following folders:
   GeneMark-ETP/bin  
   GeneMark-ETP/tools  

Move the GeneMark-ETP folder to the desired location and  
include the path to the "tools" folder.  

For example, in BASH shell:  
```
export PATH=/path_to_ETP/tools:$PATH
```

Check for the required components and install if missing.  

## PERL and PYTHON -----------  
Python 3 is required.  
Perl is required.  

Install required Perl libraries from CPAN.  
For example, on RedHat/CentOS:  
```
yum -y install perl-App-cpanminus.noarch

cpanm Cwd
cpanm Data::Dumper
cpanm File::Path
cpanm File::Spec
cpanm File::Temp
cpanm FindBin
cpanm Getopt::Long
cpanm Hash::Merge
cpanm List::Util
cpanm MCE::Mutex
cpanm Math::Utils
cpanm Parallel::ForkManager
cpanm Statistics::LineFit
cpanm Storable
cpanm Thread::Queue
cpanm YAML
cpanm YAML::XS
cpanm threads
```

## Compiled executables  -----------  
All compiled executables are for 64-bit LINUX kernel 3.10.
The executables are compiled with static library linking and should work on many LINUX systems.

Contact us on GitHub if the provided code is incompatible with your OS.

Another option is to install the required packages independently from the GeneMark-ETP distribution
and to make executables available in the path.

The information about required third-party bioinformatics tools is in the INSTALL.details file

## Test ETP installation  -----------  
To check the installation, run script
   ./check_install.pl
from the ETP folder.

The test script takes around 15 minutes of runtime to finish all test steps.


ETP is ready to use.

For installation testing, download one of the species configuration files from the repository
  https://github.com/gatech-genemark/GeneMark-ETP-exp
and execute the code as described in the repository.

####################################################
# Additional installation details are in the file:
#      INSTALL.details
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