Requirement

  • Linux x86_64 systems.
  • Perl package BioPerl is needed for running absence module.
  • Other third-party tools that have already pre-compiled and included with TEMP2. However, you may need later versions of zlib and glibc installed, especially to get samtools and bedtools work. If TEMP2 output errors for any of the softwares below, you may need to install and have them in your PATH.

Install from Github

With git installed, simply type the following command to install TEMP2:

git clone https://github.com/weng-lab/TEMP2
ln -s $PWD/TEMP2/TEMP2 your_bin_path/

To avoid mixing the pre-compiled tools with your own versions, we do not recommend to add /TEMP2/bin to the $PATH.

Install from source code

You can also install TEMP2 after fetching source code from Release page:

tar -xzvf TEMP2.tar.gz
cd TEMP2
ln -s $PWD/TEMP2 your_bin_path/

Test data

TEMP2 integrates a tested dataset in /TEMP2/test/ To test if TEMP2 is successfully installed, you can run the command below:

cd TEMP2/test
TEMP2 insertion -l test.1.fastq.gz -r test.2.fastq.gz -I bwa_index/chr2L -g chr2L.fa -R transposon.fa -t rmsk.bed -o test_output -c 2

This command takes around 2 minutes with 2 avaiable CPU. A successul installation should outputs test.insertion.bed and test.soma.summary.txt in the folder test_output, which contains detected insertions and estimated de novo insertion number per genome respectively.