Installation

Before your start

The most common cause of a failed run is a missing package or dependency. We provide two paths to simplify the task of downloading and manual install of all required dependencies: an install script (INSTALL.py) and a frozen binary. See below sections for further details.

Prerequisites

MetAMOS has several dependencies/prerequisites, the large majority of which are automatically downloaded and installed when running INSTALL.py (see next section). In addition, several dependencies/prerequisites are not installed by INSTALL.py and must be available on your system:

• Java (6+)
• perl (5.8.8+)
• python (2.7.3+)
• R (2.11.1+ with PNG support)
• gcc (4.7+ for full functionality)
• curl
• wget

Here is a list of currently supported Operating Systems:

1. Mac OSX (10.7 or newer)
2. Linux 64-bit (tested on CentOS, Fedora, RedHat, OpenSUSE and Ubuntu)

And here is a current list of required packages/libs installed by metAMOS:

1. Perl

   • File::Copy::Link
   • Statistics::Descriptive
   • Time::Piece
   • XML::Parser
   • XML::Simple

2. Python

   • Cython
   • matplolib (1.3.0, newer versions may not work)
   • NumPy
   • psutil (0.6.1, newer versions may not work)
   • PySam
   • setuptools

3. Other

   • Boost
   • cmake
   • Jellyfish
   • SparseHash

Automated installation

MetAMOS contains an automated installation script which installs MetAMOS along with required Python dependencies, third party software and necessary data files. If you encounter issues during installation, you can try installing the required dependencies manually and re-running INSTALL.py. If you continue to encounter issues, please provide the output from INSTALL.py as a new issue.

To download the software release package:

$ wget https://github.com/marbl/metAMOS/archive/v1.5rc3.zip

If you see a certificate not trusted error, you can add the following option to wget:

$ --no-check-certificate

And if wget not available, you can use curl instead:

$ curl -L https://github.com/marbl/metAMOS/archive/v1.5rc3.zip > v1.5rc3.zip

You can also browse the https://github.com/marbl/MetAMOS/tree/v1.5rc3 and click on Downloads.

Once downloaded, extract to unpack:

$ unzip v1.5rc3.zip

Change to MetAMOS directory:

$ cd metAMOS-v1.5rc3

Once inside the MetAMOS directory, run:

$ python INSTALL.py core

This will download and install the external dependencies which may take minutes or hours to download depending on your connection speed. metAMOS supports workflows to install subsets of tools for faster installation. By default only the core dependencies are installed.

To install iMetAMOS run:

$ python INSTALL.py iMetAMOS

Also, you can run:

$ python INSTALL.py help

to get a listing of available workflows and programs. You can specify either workflows or programs as arguments to INSTALL.py. For example, to install the core workflow plus PhyloSift, run:

$ python INSTALL.py core phylosift

To install the programs which are part of the optional workflow run:

$ python INSTALL.py optional

If all dependencies are downloaded (including optional/deprecated ones), this will take quite awhile to complete (plan on a few hours to 2 days).

Running the test suite

MetAMOS comes with a comprehensive test suite to make sure that installation has succeeded on your system. To run a quick test and very installation succeeded run:

$ cd ./Test
$ ./run_pipeline_test.sh