2  Installation

PyPI

# Creating a virtual environment is recommended
conda create -n iobrpy python=3.11 pip -y
conda activate iobrpy

# Update pip
python -m pip install --upgrade pip

# Install iobrpy
pip install iobrpy

# Install fastp, salmon, STAR, MultiQC and samtools
# Recommended: use mamba for faster solves (if available)
mamba install -y -c conda-forge -c bioconda \
  fastp \
  salmon \
  star \
  trust4 \
  samtools=1.21

# If you don't have mamba, use conda instead
conda install -y -c conda-forge -c bioconda \
  fastp \
  salmon \
  star \
  trust4 \
  samtools=1.21

Bioconda

Prerequisite (Conda): Please install Miniconda or Anaconda first. We recommend Miniconda.

# Creating a virtual environment is recommended
conda create -n iobrpy python=3.11 -y
conda activate iobrpy

# Install iobrpy from bioconda via conda-forge + bioconda
# Recommended: use mamba for faster solves (if available)
mamba install -y -c conda-forge -c bioconda iobrpy

# If you don't have mamba, use conda instead
conda install -y -c conda-forge -c bioconda iobrpy

Docker

#Pull the published image:
docker pull hhn123123/iobrpy:latest

Mount host directories when running an analysis. Use absolute host paths and container paths in the IOBRpy command:

docker run --rm \
  -v "/absolute/path/to/data:/data:ro" \
  -v "/absolute/path/to/results:/results" \
  hhn123123/iobrpy:latest \
  iobrpy tme_profile \
    --input /data/TPM_matrix.csv \
    --output /results