Download & Installation

Compatibility

The software Convert-Pheno can be installed locally on the following operating systems:

Operating System	Supported Versions
Linux	All major distributions
macOS	macOS 10.14 (Mojave) and later
Windows	Windows Server OS

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 Docker-based installations. Most people use the CLI.

Use case	Method
CLI	1 (CPAN)
CLI (conda)	2 (CPAN in Conda env)
API	4 or 5 (Docker)
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

Linux: Required system-level libraries

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

libbz2-dev: This is the development library for bzip2, which is used for data compression.
zlib1g-dev: This is the development library for zlib, which is another data compression library.
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++.
libssl-dev: This package is part of OpenSSL, which provides secure socket layer (SSL) capabilities. For SSL/TLS related tasks in Perl, you can use modules such as IO::Socket::SSL or Net::SSLeay, but these modules also require OpenSSL to be installed on the system.

To install it, plese see this README.

With the CPAN distribution you get:

Module
CLI

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.

Download the Miniconda installer for Linux with the following command:

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

Run the installer:
```
bash Miniconda3-latest-Linux-x86_64.sh
```
Follow the prompts on the installer screens.
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 Convert::Pheno

You can execute Convert::Pheno CLI by typing:

convert-pheno --help

To deactivate:

conda deactivate -n myenv

Optional: Using Convert::Pheno `Perl` module in `Python`¶

First we will download and install PyPerler

git clone https://github.com/tkluck/pyperler
cd pyperler
make install 2> install.log

Now you should be able to execute this file:

~/miniconda3/envs/myenv/lib/perl5/site_perl/auto/share/dist/Convert-Pheno/ex/python.py

This is the expected output:

{
"id": "P0007500",
"sex": {
    "id": "NCIT:C16576",
    "label": "Female"
      }
}

Feel free to copy that file and use for your own purposes.

With the non-containerized version from Github you get:

Module
CLI
APIs

Please follow the instructions provided in this README.

Containerized¶

With the containerized version you get:

Module
CLI
APIs

Method 4: From Docker HubMethod 5: With Dockerfile