Tutorial - lorenzo-arcioni/HPC-T-Annotator GitHub Wiki

The purpose of this tutorial is to show an example of execution that the user can do with sequences that he finds within this repository, on your local machine. So once the database and the Diamond software have been downloaded, using the command-line tool, proceed with code generation and start the computation.

First, we start by downloading the repository release into an empty directory on our filesystem on the HPC machine

cd empty_directory
wget https://github.com/lorenzo-arcioni/HPC-T-Annotator/releases/download/v1/hpc-t-annotator.tar.gz

And then extract it!

tar -xvzf hpc-t-annotator.tar.gz && rm hpc-t-annotator.tar.gz

After that, move to the HPC-T-Annotator directory.

cd hpc-t-annotator

And finally we run the main script with the following parameters, the computation will be completed in a few seconds.

./main.sh -i ./Tutorial/Altererythrobacter_sp/GIMP01.1.fsa_nt -t 4 -b `diamond path` -d `database path` -T blastx -p 2 -D

Once the computation is completed, you will find the output file of the calculation in the tmp directory with the name final_blast.tsv.