Quick Start¶

Prepare your project¶

Copy your FASTQ files into your project folder.

Then run HomeRun using one of the options below.

Run on SLURM (recommended)¶

If your system uses SLURM, submit the pipeline as SLURM job arrays:

path/to/submit_array.sh \
  --project /path/to/project \
  --partition partition_name \
  --conda-env conda_env_name \
  --genome-index /path/to/STARindex \
  --genome hg38

Run without SLURM¶

If you do not have access to a SLURM cluster, run HOMERun directly:

homerun --project /path/to/project --genome hg38

Or run it as a Python module:

python -m homerun --project /path/to/project --genome hg38

In these examples, hg38 is the genome identifier (homo_sapiens). Replace it with the genome appropriate for your dataset.

Something went wrong?¶

See Report an Issue for instructions on reporting bugs or unexpected output.