itsx_plutof

EOSC-Nordic service preparations (ITSx)

ITSx - stand alone software for detecting and extracting ribosomal ITS sequence regions of fungi and other eukaryotes for use in environmental sequencing (https://microbiology.se/software/itsx/).

Setup

Pre-requisites

• OPTIONAL: Singularity - install Singularity (needed to create new singularity container)

Setup steps

There are 2 options. You can build the singularity container yourself from source code OR you can use our prebuilt one.

Using a prebuilt container. This should work for most of the users

1. Navigate to a prefferred directory/environment where you want to run the software

2. Run setup bash script (downloads singularity container and creates input and output data directories)

    ./run_setup.sh

Building from source yourself.

You don't need to these steps if you're using the prebuilt container

1. Create Singularity Image File (SIF).

   sudo singularity build itsx_plutof.sif itsx_plutof.def

2. Copy SIF to HPC or any other place where you want to run the software

   scp itsx_plutof.sif example_hpc_user@example.com:

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 the pipeline using SIF (example data with run_id=11)

./itsx_plutof.sif 11