Maker

MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.

This is based on Maker version 3.01.04 Reference:- https://www.yandell-lab.org/software/maker.html

Prerequisites

blast - 2.13.0
snap - 2013_11_29
exonerate - 2.4.0
genblasta - 1.0.4
RepeatMasker - 4.1.2.p1
snoscan - 1.0
trnascan-se - 2.0.9
interproscan - 5.55_88.0

$ module load gencore
$ module load Miniconda3/4.7.10
$ conda create -p /scratch/gencore/conda3/envs/maker3 -c conda-forge perl=5.26.2
$ source activate /scratch/gencore/conda3/envs/maker3
$ wget http://weatherby.genetics.utah.edu/maker_downloads/D2BE/7CA3/067C/DC399810E1834576C76C4203FC4A/maker-3.01.04.tgz

Extract the file and switch to build directory which is ../maker/src/ and execute “perl Build.PL” to check the list of dependencies.

$ tar -xvf maker-3.01.04.tgz
$ cd maker/src/
$ perl Build.PL

Below commands solves perl dependencies

$ conda install -c bioconda   perl-io-all perl-inline-c
$ conda install -c bioconda perl-forks perl-want perl-bit-vector perl-bit-vector perl-dbd-sqlite perl-perl-unsafe-signals perl-dbd-pg
$ conda install -c bioconda   perl-bioperl-core

Below commands solves external softwares like blast, snap, exonerate etc..

$ conda install -c bioconda snap exonerate blast
$ conda install -c bioconda snoscan trnascan-se interproscan
$ conda install -c bioconda repeatmasker

Note:- if conda for repeatmasker fails, try below

$ ./Build installexes
$ conda install -c bioconda genblasta
$ conda install -c bioconda blast-legacy

Preparing the environment, you may see below message.

$ perl Build.PL
==============================================================================
STATUS MAKER v2.31.11
==============================================================================
PERL Dependencies:  VERIFIED
External Programs:  VERIFIED
External C Libraries:       VERIFIED
MPI SUPPORT:                DISABLED
MWAS Web Interface: DISABLED
MAKER PACKAGE:              CONFIGURATION OK

To build the installation proceed below

$ ./Build install
Building MAKER
Installing MAKER...
Building MAKER
Installing /scratch/gencore/software/maker2/src/../perl/lib/MAKER/ConfigData.pm
Installing /scratch/gencore/software/maker2/src/../perl/lib/Parallel/Application/MPI.pm
Installing /scratch/gencore/software/maker2/src/../perl/man/MAKER::ConfigData.3
Installing /scratch/gencore/software/maker2/src/../bin/map_data_ids
Installing /scratch/gencore/software/maker2/src/../bin/maker_map_ids
Installing /scratch/gencore/software/maker2/src/../bin/fasta_tool
Installing /scratch/gencore/software/maker2/src/../bin/iprscan2gff3
Installing /scratch/gencore/software/maker2/src/../bin/genemark_gtf2gff3
Installing /scratch/gencore/software/maker2/src/../bin/maker_functional_gff
Installing /scratch/gencore/software/maker2/src/../bin/chado2gff3
Installing /scratch/gencore/software/maker2/src/../bin/tophat2gff3
Instruction to run maker2 as normal user
===

To load the maker package.

$  module load gencore
$  module load Miniconda3/4.7.10
$  source activate /scratch/gencore/conda3/envs/maker3
$  export PATH="/scratch/gencore/.eb/2.0/software/augustus/3.4.0/bin:$PATH"
$  export PATH="/scratch/gencore/software/gmes_linux_64:$PATH"
$  export PATH="/scratch/gencore/software/ab-blast:$PATH"
$  export PATH="/scratch/gencore/software/genemark_prokaryotic:$PATH"
$  export PATH="/scratch/gencore/software/maker3/bin:$PATH"
$  maker -h

Database location for Maker

$ /scratch/Reference_Genomes/Public/maker2_datasets/