Zhou Lab @ AGIS Pan_TE

Design for linear or graph genome TE detection and annotation

Software Installation

1.Download the latest Pipeline:

git clone --recursive https://github.com/unavailable-2374/Pan_TE.git

2.Install:

cd Pan_TE
chmod 750 bin/*
echo 'export PATH=$HOME/tools/Pan_TE/bin:$PATH' >> ~/.bashrc
mamba env create -f env/pgta.yml
echo 'export PERL5LIB=$HOME/tools/Pan_TE/share:$HOME/tools/miniconda3/envs/PGTA/share/RepeatMasker:$PERL5LIB' >> ~/.bashrc
conda activate PGTA
cd submodule/ClassifyTE
conda env create -f environment.yml
cd submodule/LookLTRs
mkdir bin
cd bin
export CC=$HOME/tools/miniconda3/envs/PGTA/bin/x86_64-conda-linux-gnu-gcc
export CXX=$HOME/tools/miniconda3/envs/PGTA/bin/x86_64-conda-linux-gnu-c++
cmake ..
make look4ltrs
echo 'export PATH=$HOME/tools/Pan_TE/submodule/Look4LTRs/bin:$PATH' >> ~/.bashrc

ClassifyTE database download:

go to this link

• Click on ClassifyTE_Models.zip. This will automatically download models built with TE datasets.
• Unzip and copy all the models from "ClassifyTE_Models" directory into the folder models inside the root folder ClassifyTE

Usage

Usage:
perl $0 [options]

Example:
    perl $0 --genome genome.fasta --cpu 80 --model-dir Your_Path_To_ClassifyTE 

Parameters:
[General]
    --genome <string>         Required. Genome file in FASTA format.
    --model-dir <string>      Provide path to ClassifyTE for classification.

[Other]
    --vcf-dir <string>        Default: NA. Path for VCF, see gfa.list for format.
    --out <string>            Default: current directory. The work directory.
    -M <int>                  Memory limit (in MB), default: 0 (unlimited).
    --threads <int>           Default: 4. Number of threads, preferably in multiples of 4.
    --fragment_size <int>     Default: 40000. Length for fragment.
    --help|-h                 Display this help information.

Version: 1.0.0
USAGE