Download & Installation

Where should I install it?

Pheno-Ranker is software designed for local installation on Linux or MacOS server/workstations.

It is intended to work as a command-line-interface.

We provide several alternatives (containerized and non-containerized) for download and installation.

Which download method should I use?

It depends on which components you want to use and your level of fluency in performing installations in Linux environments. Here are our recommendations:

Use case	Perl utils	Python utils	Method
CLI	✓	✗	1 (CPAN)
CLI (conda)	✓	✗	2 (CPAN in Conda env)
CLI	✓	✓	4 or 5 (Docker; no dependencies)
Web App UI			Here

Overview of Pheno-Ranker Apps and utilities

Software Name	Language	Type	Short Description	Install Methods	Documentation URL
pheno-ranker	Perl 5	CLI	Compare cohort and patient data	Docker, GitHub, CPAN	Link
Pheno-Ranker Web App	R, JavaScript	R Shiny App	Web app user interface to the CLI	Docker	Link
Utilities:
bff-pxf-plot	Python 3	CLI	Plot summary stats on BFF/PXF files	Docker, GitHub	Link
bff-pxf-simulator	Perl 5	CLI	Generate simulated BFF/PXF data	Docker, GitHub, CPAN	Link
csv2pheno-ranker	Perl 5	CLI	Convert CSV to JSON for P-R CLI	Docker, GitHub, CPAN	Link
pheno-ranker2barcode, barcode2pheno-ranker, pheno-ranker2pdf	Python 3	CLI	Convert P-R vector to QR codes/PDF report	Docker, GitHub	Link

Non-Containerized

Method 1: From CPANMethod 2: From CPAN in a Conda environmentMethod 3: From Github

The core of software is a module implemented in Perl and it is available in the Comprehensive Perl Archive Network (CPAN). See the description here.

With the CPAN distribution you get:

• Module
• CLI (pheno-ranker)
• Utilities:
  • bff-pxf-simulator
  • csv2pheno-ranker

Linux: Required system-level libraries

Before procesing with installation, we will need to install system level dependencies:

• libperl-dev: This package contains the headers and libraries necessary to compile C or C++ programs to link against the Perl library, enabling you to write Perl modules in C or C++.

To install it, plese see this README.

With the CPAN distribution you get:

• Module
• CLI (pheno-ranker)
• Utilities:
  • bff-pxf-simulator
  • csv2pheno-ranker

Step 1: Install Miniconda

Instructions for x86_64

The following instructions work for amd64|x86_64 architectures. If you have a new Mac please use amd64.

1. Download the Miniconda installer for Linux with the following command:

   wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
   

2. Run the installer:

   bash Miniconda3-latest-Linux-x86_64.sh
   

   Follow the prompts on the installer screens.

3. Close and re-open your terminal window for the installation to take effect.

Step 2: Set Up Channels

Once you have Conda installed, set up the channels. Bioconda depends on the conda-forge and defaults channel.

Add bioconda channels with the following command:

conda config --add channels bioconda

Note: It's recommended to use a new Conda environment when installing new packages to avoid dependency conflicts. You can create and activate a new environment with the following commands:

Step 3: Installation

conda create -n myenv
conda activate myenv

(Replace myenv with the name you want to give to your environment)

Then you can to run the following commands:

conda install -c conda-forge gcc_linux-64 perl perl-app-cpanminus
#conda install -c bioconda perl-mac-systemdirectory # (MacOS only)
cpanm --notest Pheno::Ranker

You can execute Pheno::Ranker CLI by typing:

pheno-ranker --help

To deactivate:

conda deactivate -n myenv

With the non-containerized version from Github you get:

• Module
• CLI (pheno-ranker)
• Utilities:
  • bff-pxf-simulator
  • bff-pxf-plot
  • csv2pheno-ranker
  • QR code utilities

Please follow the instructions provided in this README.

Containerized

With the containerized version you get:

• Module
• CLI (pheno-ranker)
• Utilities:
  • bff-pxf-simulator
  • bff-pxf-plot
  • csv2pheno-ranker
  • QR code utilities

Method 4: From Docker HubMethod 5: With Dockerfile

Please follow the instructions provided in this README.

Please follow the instructions provided in this README.