Command line Interface

Command-line Interface

insilicoPCR can run without the JavaFX graphical interface. This is useful for automation, batch analysis, remote Linux machines, HPC environments, and workflow managers such as Nextflow or Snakemake.

Use the bundled Java runtime from the portable release so the command does not depend on a system Java installation.

Show help

From inside the extracted Linux portable release folder:

cd insilicoPCR-linux-x64
./runtime/linux/jdk/bin/java -jar insilicoPCR.jar -h

Expected help output:

usage: java -jar insilicoPCR.jar -i <input> -o <output> -p <primers> [-t
            n] [-m n] [-e value]
 -e,--evalue <value>   blastn e-value; default: 1e5
 -h,--help             Print help and usage
 -i,--input <path>     Input file/directory containing .fasta/.fastq
                       sequence(s)
 -m,--mismatches <n>   Allowed primer mismatches; default: 0
 -o,--output <dir>     Directory for output files
 -p,--primers <file>   Primer FASTA file
 -t,--threads <n>      Number of worker threads; default: available
                       processors
 -v,--version          Print version

Required options

Option	Meaning
-i, --input	Input FASTA/FASTQ file or directory
-o, --output	Output directory
-p, --primers	Primer FASTA file

Optional options

Option	Meaning
-t, --threads	Number of worker threads; default is available processors
-m, --mismatches	Allowed primer mismatches; default is 0
-e, --evalue	BLASTN e-value; default is 1e5
-v, --version	Print version
-h, --help	Print help

Example: assembly folder

./runtime/linux/jdk/bin/java \
  -jar insilicoPCR.jar \
  -i assemblies/ \
  -p primers.fasta \
  -o results/

Example: read folder

./runtime/linux/jdk/bin/java \
  -jar insilicoPCR.jar \
  -i reads/ \
  -p primers.fasta \
  -o results/ \
  -t 8 \
  -m 1

Example: one input file

./runtime/linux/jdk/bin/java \
  -jar insilicoPCR.jar \
  -i sample.fasta \
  -p primers.fasta \
  -o sample-results/

Notes

• The input path can be a single sequence file or a directory.
• The primer FASTA must follow the required -F, -R, and optional -P naming convention.
• Standard PCR and qPCR/probe assays should be run separately.
• The CLI uses the same pipeline as the graphical application.