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Installation from Source Code

  1. System Requirements<sys-label>
  2. Download EnTAP Source Code<ent-label>
  3. Installing Pipeline Software<dep-label>
  4. EnTAP Installation<entap-label>

System Requirements

  • Operating System

    • UNIX-based systems
    • Tested on 64 bit systems: ubuntu 16.04, Rocks 6.1, Centos 6.3

  • Storage Minimum

    • EnTAP Database (Gene Ontology References + UniProt Mapping + NCBI Taxonomy): 1.5Gb
    • EggNOG Databases: 24Gb
    • DIAMOND Databases: ~13Gb (with RefSeq Complete Protein + Uniprot Swiss-Prot)
    • Additional storage for files generated depending on transcriptome size: upwards of 15Gb

  • Memory

    • At least 16 Gb of RAM (will vary depending on DIAMOND database sizes). More memory is highly recommended to reduce execution times.

Dependency Check

Before continuing on in the installation process, ensure that the following dependencies are fully installed on your system:

  • C++11 compiler (GCC 4.8.1 or later)
  • CMake (3.00 or later)

  • Python (2.7.12 or later) with support for the following modules

    • Matplotlib (figures generated by EnTAP)
  • Unix wget (generally included in most distros)
  • Unix gzip/tar (generally included in most distros)

Downloading EnTAP Source Code

First, download and extract the latest release(tagged) version from GitLab: https://gitlab.com/EnTAP/EnTAP/tags

This repository contains the source code for RSEM, TransDecoder, and DIAMOND to be used with EnTAP.

Installing Pipeline Software

EnTAP leverages several software distributions within the pipeline to provide the best quality annotations. The packages used (and their current/compatible versions) can be seen below. This is not to say that newer versions will not be compatible, however they have not been tested yet with EnTAP.

Note

If the software is already installed on your system, this stage can be skipped

Supported Software:

  • RSEM (Expression Filtering with alignment file): version 1.3.3 packaged with EnTAP

    • Version 1.3.0
    • Version 1.3.3

  • TransDecoder (Frame Selection): version 5.7.1 packaged with EnTAP

    • Version 5.3.0
    • Version 5.7.1

  • DIAMOND (Similarity Search): version 2.1.8 packaged with EnTAP

    • Version 2.0.10 (minimum required DIAMOND version)
    • Version 2.1.8

  • EggNOG-mapper (Gene Family assignment): version 2.1.12 packaged with EnTAP

    • Version 2.1.12

  • InterProScan (Protein Databases): must be installed separately

    • Version 5.19

DIAMOND Installation

From root EnTAP directory...

Run the following command to install globally:

Run the following command to compile:

All set! Ensure that DIAMOND has been properly setup and add the correct path to the file. If installed globally, add 'diamond' (without quotes) to the file. If installed locally, add 'path/to/EnTAP/libs/diamond-2.1.8/bin/diamond'.

EggNOG-mapper Installation

EggNOG-mapper comes packaged with EnTAP, but can also be downloaded from the GitHub. If installing through the packaged version...

Run the following command to install globally:

All set! Ensure that EggNOG-mapper has been properly setup and add the correct path to the file. If installed globally, add 'emapper.py' (without quotes) to the file. If installed locally, add 'path/to/EnTAP/libs/eggnog-mapper-2.1.12/emapper.py'.

RSEM Installation

From root EnTAP directory...

Run the following command to install globally:

All set! Ensure that RSEM has been properly setup and add the correct path to the entap_config.txt file. If installed globally keep blank. If installed locally, add 'path/to/EnTAP/libs/RSEM-1.3.0/'.

EnTAP Installation

Once dependencies and pipeline software have been installed, you can now continue to install EnTAP!

Within the main directory, execute the following command:

This will generate a MakeFile. Then execute:

Or to install to a destination directory:

If you receive no errors, please move on to the last stage in installation, configuration.