Chapter 2 Installation and environment checks

2.1 Create a Conda environment and install IOBRpy

conda create -n iobrpy python=3.11 -y
conda activate iobrpy
conda install -y -c conda-forge -c bioconda iobrpy

2.2 Verify the installation

iobrpy --version
iobrpy --help

2.3 Create the project directory

Use the same project root throughout the tutorial:

export IOBRPY_DEMO=/analysis/IOBRpy_PRJNA1161405_demo

mkdir -p \
  "$IOBRPY_DEMO/input/fastq" \
  "$IOBRPY_DEMO/reference" \
  "$IOBRPY_DEMO/results_salmon" \
  "$IOBRPY_DEMO/results_star" \
  "$IOBRPY_DEMO/hla_typing"