Design for linear or graph genome TE detection and annotation
git clone https://github.com/unavailable-2374/Pan_TE.git
cd Pan_TE
chmod 750 bin/*
echo 'export PATH="/YOUR/PATH/TO/bin:$PATH"' >> ~/.bashrc //* like: echo 'export PATH="/public/home/soft/Pan_TE/bin:$PATH"' >> ~/.bashrc
mamba env create -f env/pgta.yml
ln -s /PATH/TO/miniconda3/envs/PGTA/bin/x86_64-conda-linux-gnu-g++ /PATH/TO/miniconda3/envs/PGTA/bin/g++
echo 'export PERL5LIB=/home/tool/Pan_TE/share:/home/tool/miniconda3/envs/PGTA/share/RepeatMasker:$PERL5LIB"' >> ~/.bashrc
conda activate PGTA
Look4LTRs intallation section:
git clone https://github.com/BioinformaticsToolsmith/Look4LTRs.git
cd Look4LTRs
mkdir bin
cd bin
cmake ..
vim ../src/Util.h add [#include <cstdint>] on the top
vim ../src/KmerHistogram.h add [#include <cstdint>] on the top
make look4ltrs
export PATH=/YOUR/PATH/TO/Look4LTRs/bin >> ~/.bashrc
ClassifyTE intallation section:
git clone https://github.com/manisa/ClassifyTE.git
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:
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