12/27/2021

Install Wget Mac

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Before you start using Yarn, you'll first need to install it on your system. There are many different ways to install Yarn, but a single one is recommended and cross-platform:

In this article, we will see how to install Microsoft Teams on Linux. Installing Microsoft Teams on Linux. Download the Teams package from the official repository for Redhat or Debian based distributions. I am using Centos 8 for demonstration, so I am downloading the rpm package.

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  • There are many different ways to install Yarn, but a single one is recommended and cross-platform: Install via npm. It is recommended to install Yarn through the npm package manager, which comes bundled with Node.js when you install it on your system. Once you have npm installed you can run the following both to install and upgrade Yarn.
  • Install and verify the package within the container and check for a GPU: pip uninstall tensorflow # remove current version pip install /mnt/tensorflow- version - tags.whl cd /tmp # don't import from source directory python -c 'import tensorflow as tf; print( 'Num GPUs Available: ', len(tf.config.listphysicaldevices('GPU')))'.

Install via npm

It is recommended to install Yarn through the npm package manager, which comes bundled with Node.js when you install it on your system.

Once you have npm installed you can run the following both to install and upgrade Yarn:

To install and configure wget for Windows: Download wget for Windows and install the package. Copy the wget.exe file into your C: Windows System32 folder. Open the command prompt (cmd.exe) and run wget to see if it is installed. Here is a quick video showing you how to download wget on windows 10. To install wget, run the following command in macOS terminal (Applications-Utilities-Terminal) sudo port install wget. To see what files were installed by wget, run: port contents wget. To later upgrade wget, run: sudo port selfupdate && sudo port upgrade wget.

Alternatives

Click to expand / collapse

Alpine

On Alpine Linux (3.6+), you can install Yarn with apk.

Currently, there are no Alpine packages available for RC or nightly builds of Yarn. Please use the tarball:

Installation Script

One of the easiest ways to install Yarn on macOS and generic Unix environmentsis via our shell script. You can install Yarn by running the following code inyour terminal:

The installation process includes verifying a GPG signature.View the source on GitHub

You can also specify a version by running the following code in your terminal:

See the releases for possible versions.

Manual Install via tarball

You can install Yarn by downloading a tarball andextracting it anywhere.

Before extracting Yarn, it is recommended that you verify the tarball using GPG:

Path Setup

Install Wget Mac Without Brew

If Yarn is not found in your PATH, follow these steps to add it and allow it to be run from anywhere.

Note: your profile may be in your .profile, .bash_profile, .bashrc, .zshrc, etc.

  1. Add this to your profile: export PATH='$PATH:/opt/yarn-[version]/bin' (the path may vary depending on where you extracted Yarn to)
  2. In the terminal, log in and log out for the changes to take effect

To have access to Yarn’s executables globally, you will need to set up the PATH environment variable in your terminal. To do this, add export PATH='$PATH:`yarn global bin`' to your profile, or if you use Fish shell, simply run the command set -U fish_user_paths (yarn global bin) $fish_user_paths

Arch Linux

On Arch Linux, Yarn can be installed through the official package manager.

Currently, there are no Arch packages available for RC or nightly builds of Yarn. Please use the tarball:

Installation Script

One of the easiest ways to install Yarn on macOS and generic Unix environmentsis via our shell script. You can install Yarn by running the following code inyour terminal:

The installation process includes verifying a GPG signature.View the source on GitHub

You can also specify a version by running the following code in your terminal:

See the releases for possible versions.

Manual Install via tarball

You can install Yarn by downloading a tarball andextracting it anywhere.

Before extracting Yarn, it is recommended that you verify the tarball using GPG:

Path Setup

If Yarn is not found in your PATH, follow these steps to add it and allow it to be run from anywhere.

Note: your profile may be in your .profile, .bash_profile, .bashrc, .zshrc, etc.

  1. Add this to your profile: export PATH='$PATH:/opt/yarn-[version]/bin' (the path may vary depending on where you extracted Yarn to)
  2. In the terminal, log in and log out for the changes to take effect

To have access to Yarn’s executables globally, you will need to set up the PATH environment variable in your terminal. To do this, add export PATH='$PATH:`yarn global bin`' to your profile, or if you use Fish shell, simply run the command set -U fish_user_paths (yarn global bin) $fish_user_paths

CentOS / Fedora / RHEL

On CentOS, Fedora and RHEL, you can install Yarn via our RPM package repository.

If you do not already have Node.js installed, you should also configurethe NodeSource repository:

Then you can simply:

Currently, there are no RPM packages available for RC or nightly builds of Yarn. Please use the tarball:

Installation Script

One of the easiest ways to install Yarn on macOS and generic Unix environmentsis via our shell script. You can install Yarn by running the following code inyour terminal:

The installation process includes verifying a GPG signature.View the source on GitHub

You can also specify a version by running the following code in your terminal:

Install Wget On Mac

See the releases for possible versions.

Manual Install via tarball

You can install Yarn by downloading a tarball andextracting it anywhere.

Before extracting Yarn, it is recommended that you verify the tarball using GPG:

Path Setup

If Yarn is not found in your PATH, follow these steps to add it and allow it to be run from anywhere.

Note: your profile may be in your .profile, .bash_profile, .bashrc, .zshrc, etc.

  1. Add this to your profile: export PATH='$PATH:/opt/yarn-[version]/bin' (the path may vary depending on where you extracted Yarn to)
  2. In the terminal, log in and log out for the changes to take effect

To have access to Yarn’s executables globally, you will need to set up the PATH environment variable in your terminal. To do this, add export PATH='$PATH:`yarn global bin`' to your profile, or if you use Fish shell, simply run the command set -U fish_user_paths (yarn global bin) $fish_user_paths

Debian / Ubuntu

On Debian or Ubuntu Linux, you can install Yarn via our Debian packagerepository. You will first need to configure the repository:

On Ubuntu 16.04 or below and Debian Stable, you will also need to configure the NodeSource repository to get a new enough version of Node.js.

Then you can simply:

Note: Ubuntu 17.04 comes with cmdtest installed by default. If you’re getting errors from installing yarn, you may want to run sudo apt remove cmdtest first. Refer to this for more information.

If using nvm you can avoid the node installation by doing:

Note: Due to the use of nodejs instead of node name in some distros, yarn might complain about node not being installed. A workaround for this is to add an alias in your .bashrc file, like so: alias node=nodejs. This will point yarn to whatever version of node you decide to use.

Path Setup

If Yarn is not found in your PATH, follow these steps to add it and allow it to be run from anywhere.

Note: your profile may be in your .profile, .bash_profile, .bashrc, .zshrc, etc.

  1. Add this to your profile: export PATH='$PATH:/opt/yarn-[version]/bin' (the path may vary depending on where you extracted Yarn to)
  2. In the terminal, log in and log out for the changes to take effect

To have access to Yarn’s executables globally, you will need to set up the PATH environment variable in your terminal. To do this, add export PATH='$PATH:`yarn global bin`' to your profile, or if you use Fish shell, simply run the command set -U fish_user_paths (yarn global bin) $fish_user_paths

Gentoo Linux

On Gentoo Linux, you can install Yarn with portage.

Currently, there are no Gentoo packages available for RC or nightly builds of Yarn. Please use the tarball:

Installation Script

One of the easiest ways to install Yarn on macOS and generic Unix environmentsis via our shell script. You can install Yarn by running the following code inyour terminal:

The installation process includes verifying a GPG signature.View the source on GitHub

You can also specify a version by running the following code in your terminal:

See the releases for possible versions.

Manual Install via tarball

You can install Yarn by downloading a tarball andextracting it anywhere.

Before extracting Yarn, it is recommended that you verify the tarball using GPG:

Path Setup

If Yarn is not found in your PATH, follow these steps to add it and allow it to be run from anywhere.

Install Wget Mac

Note: your profile may be in your .profile, .bash_profile, .bashrc, .zshrc, etc.

  1. Add this to your profile: export PATH='$PATH:/opt/yarn-[version]/bin' (the path may vary depending on where you extracted Yarn to)
  2. In the terminal, log in and log out for the changes to take effect

To have access to Yarn’s executables globally, you will need to set up the PATH environment variable in your terminal. To do this, add export PATH='$PATH:`yarn global bin`' to your profile, or if you use Fish shell, simply run the command set -U fish_user_paths (yarn global bin) $fish_user_paths

macOS

Homebrew

You can install Yarn through the Homebrew package manager.This will also install Node.js if it is not already installed.

If you use nvm or similar, you should ensure that your PATH lists nvm’s shims before the version of Node.js installed by Homebrew.

MacPorts

You can install Yarn through MacPorts.This will also install Node.js if it is not already installed.

Installation Script

One of the easiest ways to install Yarn on macOS and generic Unix environmentsis via our shell script. You can install Yarn by running the following code inyour terminal:

The installation process includes verifying a GPG signature.View the source on GitHub

You can also specify a version by running the following code in your terminal:

See the releases for possible versions.

Manual Install via tarball

You can install Yarn by downloading a tarball andextracting it anywhere.

Before extracting Yarn, it is recommended that you verify the tarball using GPG:

Currently, there are no Homebrew or MacPorts packages available for RC or nightly builds of Yarn. Please use the tarball:

Installation Script

One of the easiest ways to install Yarn on macOS and generic Unix environmentsis via our shell script. You can install Yarn by running the following code inyour terminal:

The installation process includes verifying a GPG signature.View the source on GitHub

You can also specify a version by running the following code in your terminal:

See the releases for possible versions.

Manual Install via tarball

You can install Yarn by downloading a tarball andextracting it anywhere.

Before extracting Yarn, it is recommended that you verify the tarball using GPG:

Path Setup

If Yarn is not found in your PATH, follow these steps to add it and allow it to be run from anywhere.

Note: your profile may be in your .profile, .bash_profile, .bashrc, .zshrc, etc.

  1. Add this to your profile: export PATH='$PATH:/opt/yarn-[version]/bin' (the path may vary depending on where you extracted Yarn to)
  2. In the terminal, log in and log out for the changes to take effect

To have access to Yarn’s executables globally, you will need to set up the PATH environment variable in your terminal. To do this, add export PATH='$PATH:`yarn global bin`' to your profile, or if you use Fish shell, simply run the command set -U fish_user_paths (yarn global bin) $fish_user_paths

Upgrade Yarn

Yarn will warn you if a new version is available.To upgrade Yarn, you can do so with Homebrew.

Solus

On Solus, you can install yarn via the Solus repository.

Currently, there are no Solus packages available for RC or nightly builds of Yarn. Please use the tarball:

Install wget mac homebrew

Installation Script

One of the easiest ways to install Yarn on macOS and generic Unix environmentsis via our shell script. You can install Yarn by running the following code inyour terminal:

The installation process includes verifying a GPG signature.View the source on GitHub

You can also specify a version by running the following code in your terminal:

See the releases for possible versions.

Manual Install via tarball

You can install Yarn by downloading a tarball andextracting it anywhere.

Before extracting Yarn, it is recommended that you verify the tarball using GPG:

Path Setup

If Yarn is not found in your PATH, follow these steps to add it and allow it to be run from anywhere.

Note: your profile may be in your .profile, .bash_profile, .bashrc, .zshrc, etc.

Install
  1. Add this to your profile: export PATH='$PATH:/opt/yarn-[version]/bin' (the path may vary depending on where you extracted Yarn to)
  2. In the terminal, log in and log out for the changes to take effect

To have access to Yarn’s executables globally, you will need to set up the PATH environment variable in your terminal. To do this, add export PATH='$PATH:`yarn global bin`' to your profile, or if you use Fish shell, simply run the command set -U fish_user_paths (yarn global bin) $fish_user_paths

Windows

There are three options for installing Yarn on Windows.

Download the installer

This will give you a .msi file that when run will walk you through installingYarn on Windows.

If you use the installer you will first need to installNode.js.

Download InstallerDownload Installer (RC)Download Installer (Nightly)

Install via Chocolatey

Install Wget In Mac

Chocolatey is a package manager for Windows.You can install Chocolatey by followingthese instructions.

Once you have Chocolatey installed, you may install yarn by running thefollowing code in your console:

This will also ensure that you have Node.js installed.

Install via Scoop

Scoop is a command-line installer for Windows.You can install Scoop by followingthese instructions.

Once you have Scoop installed, you may install yarn by running thefollowing code in your console:

If Node.js is not installed, scoop will give you a suggestion to install it.Example:

Notice

Please whitelist your project folder and the Yarn cache directory (%LocalAppData%Yarn) in your antivirus software, otherwise installing packages will be significantly slower as every single file will be scanned as it’s written to disk.

Alternatives

If you are using another OS or one of the other options specific to your OSwill not work for you, there are a couple of alternatives. You will need toinstall Node.js if you don’t already have it installed.

On common Linux distributions such as Debian, Ubuntu and CentOS, it isrecommended to install Yarn via our packages instead.

Installation Script

Install Wget Mac Brew

One of the easiest ways to install Yarn on macOS and generic Unix environmentsis via our shell script. You can install Yarn by running the following code inyour terminal:

The installation process includes verifying a GPG signature.View the source on GitHub

You can also specify a version by running the following code in your terminal:

See the releases for possible versions.

Manual Install via tarball

You can install Yarn by downloading a tarball andextracting it anywhere.

Before extracting Yarn, it is recommended that you verify the tarball using GPG:

Path Setup

Unix/Linux/macOS

If Yarn is not found in your PATH, follow these steps to add it and allow it to be run from anywhere.

Note: your profile may be in your .profile, .bash_profile, .bashrc, .zshrc, etc.

  1. Add this to your profile: export PATH='$PATH:/opt/yarn-[version]/bin' (the path may vary depending on where you extracted Yarn to)
  2. In the terminal, log in and log out for the changes to take effect

To have access to Yarn’s executables globally, you will need to set up the PATH environment variable in your terminal. To do this, add export PATH='$PATH:`yarn global bin`' to your profile, or if you use Fish shell, simply run the command set -U fish_user_paths (yarn global bin) $fish_user_paths

Windows

You will need to set up the PATH environment variable in your terminal to have access to Yarn’s binaries globally.

Add set PATH=%PATH%;C:.yarnbin to your shell environment.

Check installation

Check that Yarn is installed by running:

Install Wget Mac Homebrew

ColabFold / AlphaFold2_advanced on your local PC (or macOS)

Installation

For Linux

  1. Make sure curl and wget commands are already installed on your PC. If not present, you need install them at first. For Ubuntu, type sudo apt -y install curl wget.
  2. Download install_colabfold_linux.sh from this repository:$ wget https://raw.githubusercontent.com/YoshitakaMo/localcolabfold/main/install_colabfold_linux.shand run it in the directory where you want to install:$ bash install_colabfold_linux.shAbout 5 minutes later, colabfold directory will be created. Do not move this directory after the installation.
  3. Type cd colabfold to enter the directory.
  4. Modify the variables such as sequence = 'PIAQIHILEGRSDEQKETLIREVSEAISRSLDAPLTSVRVIITEMAKGHFGIGGELASK', jobname = 'test', and etc. in runner.py for your prediction. For more information, please refer to the original ColabFold / AlphaFold2_advanced.
  5. To run the prediction, type$ colabfold-conda/bin/python3.7 runner.pyin the colabfold directory. The result files will be created in the predition_<jobname>_<hash> in the colabfold directory. After the prediction finished, you may move the results from the colabfold directory.

For macOS

Caution: Due to the lack of Nvidia GPU/CUDA driver, the structure prediction on macOS are 5-10 times slower than on Linux+GPU. For the test sequence (58 a.a.), it may take 30 minutes. However, it may be useful to play with it before preparing Linux+GPU environment.

You can check whether your Mac is Intel or Apple Silicon by typing uname -m on Terminal.

$ uname -m x86_64 # Intelarm64 # Apple Silicon

Please use the correct installer for your Mac.

For Mac with Intel CPU

  1. Install Homebrew if not present:$ /bin/bash -c '$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)'
  2. Install wget command using Homebrew:$ brew install wget
  3. Download install_colabfold_intelmac.sh from this repository:$ wget https://raw.githubusercontent.com/YoshitakaMo/localcolabfold/main/install_colabfold_intelmac.shand run it in the directory where you want to install:$ bash install_colabfold_intelmac.shAbout 5 minutes later, colabfold directory will be created. Do not move this directory after the installation.
  4. The rest procedure is the same as 'For Linux'.

For Mac with Apple Silicon (M1 chip)

Note: This installer is experimental because most of the dependent packages are not fully tested on Apple Silicon Mac.

  1. Install Homebrew if not present:$ /bin/bash -c '$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)'
  2. Install wget command using Homebrew:$ brew install wget
  3. Install miniforge command using Homebrew:$ brew install --cask miniforge
  4. Download install_colabfold_M1mac.sh from this repository:$ wget https://raw.githubusercontent.com/YoshitakaMo/localcolabfold/main/install_colabfold_M1mac.shand run it in the directory where you want to install:$ bash install_colabfold_M1mac.shAbout 5 minutes later, colabfold directory will be created. Do not move this directory after the installation.
  5. Type cd colabfold to enter the directory.
  6. Modify the variables such as sequence = 'PIAQIHILEGRSDEQKETLIREVSEAISRSLDAPLTSVRVIITEMAKGHFGIGGELASK', jobname = 'test', and etc. in runner.py for your prediction. For more information, please refer to the original ColabFold / AlphaFold2_advanced.
  7. To run the prediction, type$ colabfold-conda/bin/python3.8 runner.pyin the colabfold directory. The result files will be created in the predition_<jobname>_<hash> in the colabfold directory. After the prediction finished, you may move the results from the colabfold directory.

A Warning message appeared when you run the prediction:

Install Wget Mac M1

This message is due to Apple Silicon, but I think we can ignore it.

Advantages of LocalColabFold

  • Structure inference and relaxation will be accelerated if your PC has Nvidia GPU and CUDA drivers.
  • No Time out (90 minutes and 12 hours), No GPU limitations.
  • You don't need prepare the large database required for native AlphaFold2.

FAQ

  • What else do I need to do before installation? Do I need sudo privileges?
  • No, except for installation of curl and wget commands.
  • Do I need to prepare the large database such as PDB70, BFD, Uniclust30, MGnify...?
  • No. it is not necessary. Generation of MSA is performed by the MMseqs2 web server, just as implemented in ColabFold.
  • Are the pLDDT score and PAE figures available?
  • Yes, they will be generated just like the ColabFold.
  • Is it possible to predict homooligomers and complexes?
  • Yes, the sequence input is the same as ColabFold. See ColabFold / AlphaFold2_advanced.
  • Is it possible to create MSA by jackhmmer?
  • No, it is not currently supported.
  • I want to run the predictions step-by-step like Google Colab.
  • You can use VSCode and Python plugin to do the same. See https://code.visualstudio.com/docs/python/jupyter-support-py.
  • Is this available on Windows 10?
  • You can run LocalColabFold on your Windows 10 with WSL2.

Tutorials & Presentations

  • ColabFold Tutorial presented at the Boston Protein Design and Modeling Club. [video][slides].

Acknowledgments

  • The original colabfold was created by Sergey Ovchinnikov (@sokrypton), Milot Mirdita (@milot_mirdita) and Martin Steinegger (@thesteinegger).

GitHub

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