Installation from Source Code
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:
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…
cd libs/
tar -xvzf diamond-v2.1.8.tar.gz
cd diamond-v2.1.8
mkdir bin
cd bin
cmake ..
Run the following command to install globally:
make install
Run the following command to compile:
make
All set! Ensure that DIAMOND has been properly setup and add the correct path to the entap_config.ini 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…
cd libs/
tar -xvzf eggnog-mapper-2.1.12.tar.gz
cd eggnog-mapper-2.1.12
Run the following command to install globally:
python setup.py install
All set! Ensure that EggNOG-mapper has been properly setup and add the correct path to the entap_config.ini 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…
cd libs/
tar -xvzf RSEM-v1.3.3.tar.gz
cd RSEM-v1.3.3
make
make ebseq
Run the following command to install globally:
make install
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:
cmake CMakeLists.txt
This will generate a MakeFile. Then execute:
make
Or to install to a destination directory:
cmake CMakeLists.txt -DCMAKE_INSTALL_PREFIX=/destination/dir
make install
If you receive no errors, please move on to the last stage in installation, configuration.