primerlab batch-run

CLI reference for the primerlab batch-run command

Run multiple primer designs in batch mode.

Synopsis

primerlab batch-run [options]

Options

Option	Short	Description
--configs	-c	Directory with configs OR comma-separated paths
--fasta	-f	Multi-FASTA file with multiple sequences
--config		Shared config for multi-FASTA mode
--output	-o	Output directory (default: ./batch_output)
--export	-e	Export format for summary (default: xlsx)
--continue-on-error		Continue if some designs fail

Modes

Mode 1: Multiple Config Files

# From directory
primerlab batch-run --configs ./configs/ --output ./results/

# From specific files
primerlab batch-run --configs config1.yaml,config2.yaml --output ./results/

Mode 2: Multi-FASTA with Shared Config

primerlab batch-run --fasta genes.fasta --config shared.yaml --output ./results/

Examples

Batch from Directory

primerlab batch-run \
  --configs ./project_configs/ \
  --output ./batch_results/ \
  --continue-on-error

Multi-FASTA Mode

primerlab batch-run \
  --fasta examples/multi_sequences.fasta \
  --config examples/pcr_standard.yaml \
  --output ./batch_results/

Output

• Individual results per sequence
• batch_summary.xlsx - Combined Excel summary
• Console summary with success/fail stats