Download & Installation

Compatibility

The Pheno-Ranker Perl command-line interface is tested on Linux, macOS, and Windows via GitHub Actions.

Operating System	Support
Linux	Recommended for CLI, Docker, and utility workflows
macOS	Supported for non-containerized CLI use
Windows	Supported for the Perl CLI; use Docker, WSL, or a Perl environment such as Strawberry Perl

Python utilities under utils/ and external R plotting scripts are not part of the CPAN-centered Windows test matrix. For those workflows, Docker or a GitHub checkout is recommended.

This page keeps the installation-method nomenclature used in the paper supplementary information:

Code	Installation method
D	Docker
G	GitHub
C	CPAN

Which download method should I use?

It depends on which component you need and whether you want to manage Perl/Python dependencies yourself. The D, G, and C codes follow Additional file 2, Supporting Table 2.

Component	Recommended install methods
pheno-ranker CLI	D, G, C
bff-pxf-simulator	D, G, C
csv2pheno-ranker	D, G, C
bff-pxf-plot	D, G
QR-code/PDF utilities	D, G
Web App UI	D; see Pheno-Ranker UI

Non-Containerized

Use this path when you want to run pheno-ranker directly from CPAN, GitHub, Conda, or your own Perl environment.

The CPAN distribution includes:

• Pheno::Ranker
• pheno-ranker
• bff-pxf-simulator
• csv2pheno-ranker

Detailed instructions:

• non-containerized/README.md

Method 1: From CPAN (C)

Recommended when you only need the installable Perl CLI and the CPAN-packaged utilities.

See the CPAN instructions in non-containerized/README.md.

Method 2: From CPAN in a Conda Environment (C)

Recommended when you want the CPAN installation isolated from your system Perl.

See the Conda instructions in non-containerized/README.md.

Method 3: From GitHub (G)

Recommended when you need the repository utilities, examples, tests, or development version.

See the GitHub checkout instructions in non-containerized/README.md.

Containerized

Use this path when you want a reproducible environment with Perl dependencies and Python utilities preinstalled.

The Docker image includes:

• Pheno::Ranker
• pheno-ranker
• bff-pxf-simulator
• bff-pxf-plot
• csv2pheno-ranker
• QR-code utilities

Detailed instructions:

• docker/README.md

Method 4: From Docker Hub (D)

Recommended when you want the prebuilt container image.

See the Docker Hub instructions in docker/README.md.

Method 5: With Dockerfile (D)

Recommended when you want to build the container image yourself.

See the Dockerfile instructions in docker/README.md.