/protax_fungi_plutof_pub

EOSC-Nordic service preparations (PROTAX-fungi)

Primary LanguageShell

protax_fungi_plutof

EOSC-Nordic service preparations (PROTAX-fungi)

PROTAX-fungi - stand alone tool for probabilistic taxonomic placement of fungal ITS sequences (https://github.com/psomervuo/protaxfungi).

Setup

Pre-requisites

  • OPTIONAL: Singularity - install Singularity (needed to create new singularity container)
  • OPTIONAL: VSEARCH - download VSEARCH binary (needed to update supporting files)

Setup steps

  1. OPTIONAL: Create Singularity Image File (SIF)

    sudo singularity build protax.sif protax_fungi_plutof.def

  2. OPTIONAL: Copy SIF to HPC

    scp protax.sif example_hpc_user@example.com:

  3. Run setup bash script (downloads singularity container and supporting data files, creates input and output data directories)

    ./run_setup.sh

  4. OPTIONAL: prepare updated supporting data files (udb) needed by PROTAX-fungi (location of these files should be in the db_files/ folder)

    wget https://github.com/torognes/vsearch/releases/download/v2.15.1/vsearch-2.15.1-linux-x86_64.tar.gz
tar xzf vsearch-2.15.1-linux-x86_64.tar.gz
rm vsearch-2.15.1-linux-x86_64.tar.gz
wget https://files.plutof.ut.ee/public/orig/A9/11/A911815A6691B3F74EACA42A20605CEB680424F01553E65D1EF3A6767BBCA22B.zip
unzip A911815A6691B3F74EACA42A20605CEB680424F01553E65D1EF3A6767BBCA22B.zip
rm A911815A6691B3F74EACA42A20605CEB680424F01553E65D1EF3A6767BBCA22B.zip
./vsearch-2.15.1-linux-x86_64/bin/vsearch -makeudb_usearch db_files/its1.fa -output db_files/its1.udb
./vsearch-2.15.1-linux-x86_64/bin/vsearch -makeudb_usearch db_files/its2.fa -output db_files/its2.udb
./vsearch-2.15.1-linux-x86_64/bin/vsearch -makeudb_usearch db_files/itsfull.fa -output db_files/itsfull.udb
./vsearch-2.15.1-linux-x86_64/bin/vsearch -makeudb_usearch db_files/sintaxits1train.fa -output db_files/sintaxits1.udb
./vsearch-2.15.1-linux-x86_64/bin/vsearch -makeudb_usearch db_files/sintaxits2train.fa -output db_files/sintaxits2.udb
./vsearch-2.15.1-linux-x86_64/bin/vsearch -makeudb_usearch db_files/sintaxitsfulltrain.fa -output db_files/sintaxitsfull.udb

PROTAX-fungi: running the analysis (OPTIONAL: This could be done through sbatch slurm scripts)

NB! The script expects input files in FASTA format, named as source_[run_id] and placed in indata/ directory.

  1. Run PROTAX-fungi using SIF (example data with run_id=11) 
    ./protax.sif /run_protax_plutof.sh 11 itsfull 90