Linux, Mac, or Windows?
helical software has been compiled specially for 64 bit Linux, Mac, and Windows including Intel and Apple Silicon (M1,M2) Macs.
The installation script (see the Getting Started - Helical CLI section from the sidebar) automatically chooses the appropriate binary to install based on the detected operating system and CPU architecture.
Primarily production workloads are run on Linux operating systems, and this is where we have the most experience. The Helical Company team also primarily uses Mac OS (which has Unix/Linux "underneath"), and the
helical software functions identically on Mac OS as for Linux, which makes it a great system for prototyping, tutorials, and even some production workloads.
Regardless of the operating system you choose to use, we heavily recommend making use of VSCode. It has built in support for terminals, a huge number of extensions and language support (for bash, Julia, R, and many others), SSH and remote connection/editing capabilities (including drag/drop copy of data).
Mac OS Environment
To get the most of your Mac with
helical and genetic/genomic evaluations we suggest installing a few tools (in addition to VSCode).
XCode Command Line Tools
By default MacOS does not come with some basic developer tools like
git. These can be installed by installing the XCode command line tools. Rather than installing XCode (which is ~40 GB in size), you can just install the command line tools by running the following command from terminal:
Once run, a prompt will appear asking if you want to install the Command Line Tools. Follow the instructions to complete the installation. Once complete, tools like
git will be accessible from the MacOS terminal.
Homebrew is a package manager for Mac OS and is helpful for installing a variety of GNU and other tools that are useful in data processing. You can alternatively use Macports if you are sadistic or enjoy very long coffee breaks while you wait for it to update.
Here is a short guide to install Homebrew on Mac OS:
- Open terminal on your MacOS.
- Run the following command to install Homebrew:
$ /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
- Follow the on-screen instructions to complete the installation process.
GNU Core Utilities
While MacOS comes with many of the GNU toolset, they are not always 100% identical to those found on Linux, and we suggest installing the
After installing Homebrew, run the following command in Terminal to install the GNU core utilities:
$ brew install coreutils
The GNU versions of the core utilities are prefixed with
g. Some other helpful packages (including GNU
gsed and GNU
gawk) can be installed with
$ brew install datamash lbzip2 gnu-sed gawk
There are several ways to run
helical on Windows.
One way is using the command prompt
cmd utility. It is probably the least elegant approach and lacks the Unix tools and functionality that
helical complements well, so we do not suggest this.
Windows Subsystem for Linux (WSL)
The best approach is to use the new built-in Linux environment Windows Subsystem for Linux (WSL). WSL is the best option because it provides a native Linux environment which enables full functionality of the
Installation is not super straightforward depending on your Windows operating system version but the instructions can be found here: https://learn.microsoft.com/en-us/windows/wsl/install
We recommend installing the latest Ubuntu OS.
Additional best practices for WSL set up can be found here: https://learn.microsoft.com/en-us/windows/wsl/setup/environment
A tutorial on running VSCode in the WSL environment is here: https://learn.microsoft.com/en-us/windows/wsl/tutorials/wsl-vscode
Once installed, you can install
helical as normal from the WSL (Ubuntu) terminal.
Cygwin is a collection of tools that provide a Unix-like environment on Windows. Here is how to install Cygwin on a Windows machine:
- Go to the Cygwin website (https://cygwin.com/).
- Click on the "Install" link in the top menu to download the setup program.
- Save the setup program to your computer.
- Double-click on the setup program to start the installation process.
- Follow the on-screen instructions to complete the installation.
- When prompted, select the packages you want to install. You can select packages by category or search for specific packages by name. Be sure to select the "Base" category, as it includes the essential packages needed to run Cygwin. Click "Next" to continue. The installer will download and install the selected packages.
- Wait for the installation to complete.
- Once the installation is complete, you can launch the Cygwin Terminal by clicking on the "Cygwin" icon on your desktop or by running the "Cygwin64 Terminal" program from the Start menu.
That's it! You should now have a working installation of Cygwin on your Windows machine. You can use the Cygwin Terminal to run Unix-like commands and tools just as you would on a Unix system, including installation of the
helical tool as normal.