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
-
OPTIONAL: Create Singularity Image File (SIF)
sudo singularity build protax.sif protax_fungi_plutof.def -
OPTIONAL: Copy SIF to HPC
scp protax.sif example_hpc_user@example.com: -
Run setup bash script (downloads singularity container and supporting data files, creates input and output data directories)
./run_setup.sh -
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.
- Run PROTAX-fungi using SIF (example data with run_id=11)
./protax.sif /run_protax_plutof.sh 11 itsfull 90