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 in which components you want to use and your fluency in performing installations on Linux environments.

The CPAN based installation (Method 1) is the easier one.

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

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.