yifan-grace-tang/antismash-installation

Anti-SMASH Installation Instructions

Installation Guide

Please read through this entire guide before getting started as it will save you a lot of time troubleshooting errors later on.

Even if you have never installed similar softwares on your computer before, you should be able to install antiSMASH as long as you read this guide thoroughly.

Before You Get Started

• Unless otherwise specified, use the copy button feature on GitHub ONLY, do not attempt to manually type commands into your terminal.

• If commands are expected to take a long time to complete they will be indicated with this icon ⌛. This means that either you should wait until a confirmation/continue action or wait until you can type again. You should see something like this when you are able to type again:

For Macbook Pro

(base) username@your-mbp ~ % |

For Macbook Air

(base) username@your-air ~ % |

For a Windows Computer (Powershell)

PS C:\Users\username> |

For a Windows Computer (Ubuntu)

(base) username@Name:~$ |

• When editing text in the terminal window you cannot highlight a particular area and delete with your keyboard. Instead to delete a portion of your command you must use your left arrow and navigate to the portion you want to edit

Installation Steps

Important

If you have installed BiG-SCAPE as detailed in these instructions then you can skip straight to antiSMASH Installation for your respective platform

Follow the links for your platform do not use Windows instructions for Mac or vice-versa. These steps are dependent on each other so follow them sequentially.

For Mac:

1. 🐍 Miniconda Installation
2. 🌱 antiSMASH Installation

For Windows:

1. 🐧 WSL Installation
2. 🐍 Miniconda Installation
3. 🌱 antiSMASH Installation

Mac Based Installation

Follow these instructions only if you are using a Mac. The expectation is that you first do conda installation, then antismash installation.

🐍 Miniconda Installation (Mac)

Warning

Follow the file download instructions very carefully! If you don't download the right file, there will be lots of troubleshooting.

Note

Miniconda is also refered to as conda and those terms will be used interchangibly in this installation guide.

1. Check if conda is already installed on your computer. Paste in your terminal :

conda -V

2. If the conda is already installed, you will see a message similar to the one below (versions can differ). Proceed to the antiSMASH Installation section.

conda 24.5.0

3. If the conda is not installed, then you will see the message below - proceed to step 4:

zsh: command not found: conda

4. Navigate to this link and download the installer version as specificied in the images DO NOT SELECT ANY OTHER INSTALLER. Click the link under the Name field to begin installation

5. Open a new terminal window and copy-paste the command below:

cd downloads

6. ⌛ Paste into your terminal:

bash Miniconda3-latest-MacOSX-x86_64.sh

7. You will now be prompted for a series of agreements that you must accept from your terminal. These are included below:

Here type the word 'yes' and click enter

When you see the Terms of Service (TOS) use your down arrow key to get through the text

After you finish scrolling through the TOS type the word 'yes' to move on

Complete the installation by clicking the 'return' key

8. Close your terminal window and open a new terminal window.

9. Check if conda is successfully installed on your computer. Paste in your terminal:

conda -V

10. If the conda is sucessfully installed, you will see a message similar to the one below (versions can differ). Proceed to the antiSMASH Installation section.

conda 24.5.0

🌱 antiSMASH Installation (Mac)

1. From your terminal copy and paste the below command:

conda config --add channels defaults && conda config --add channels bioconda && conda config --add channels conda-forge && conda config --set channel_priority strict

2. ⌛ Copy and paste this command:

conda create -n antismash antismash

3. During the above command you will be asked to confirm the installation, type 'yes' and click enter as shown below:

insert image

3. Copy and paste this command:

conda activate antismash

4. ⌛ Copy and paste this command:

download-antismash-databases

Windows Based Installation

Follow these instructions only if you are using a Windows machine. The expectation is that you first do wsl installation, then conda installation, then antismash installation.

🐧 WSL Installation (Windows)

1. Check if wsl is already installed on your computer. Look through your applications and see if there is an ubuntu application on your machine.

2. If you see ubuntu on your machine proceed to the Miniconda Installation section.

3. If you cannot find the ubuntu application proceed to step 4.

4. Find your Windows PowerShell application and run as administrator. You will be asked to confirm if you "want to allow this app to make changes to your device" - click yes.

5. ⌛ Paste into your powershell:

wsl --install

6. Restart your computer for the changes to activate.

7. After your computer restarts, the ubuntu application should now be available, open this app:

8. The first time you open this app you will be prompted to create a username and password. This is in no way tied to your Windows account so choose whatever you would like. This input will look like below:

Type username, click enter, type password, click enter, retype password, click enter.

Warning

Note down the password that you create, it will be used later on.

Note

You will not be able to see the password you type, so just type your password and click enter.

9. After you create your username and password you can now close the ubuntu app and proceed to Miniconda Installation

🐍 Miniconda Installation (Windows)

Warning

Follow the file download instructions very carefully! If you don't download the right file, there will be lots of troubleshooting.

Note

Miniconda is also refered to as conda and those terms will be used interchangibly in this installation guide.

1. Check if conda is already installed on your computer. Paste in your ubuntu :

conda -V

2. If the conda is already installed, you will see a message similar to the one below (versions can differ). Proceed to the antiSMASH Installation section.

conda 24.5.0

3. If the conda is not installed, then you will see the message below - proceed to step 4:

conda: command not found

4. Navigate to this link and download the installer version as specificied in the images DO NOT SELECT ANY OTHER INSTALLER. Click the link under the Name field to begin installation

5. Open a new ubuntu window and copy-paste the command below. Replace USERNAME with your Windows username:

cd ../../mnt/c/Users/USERNAME/Downloads

Note

To find your USERNAME you can open the powershell application and type the command $ENV:UserName and click enter. Copy the value that you see.

6. ⌛ Paste into your ubuntu:

bash Miniconda3-latest-Linux-x86_64.sh

7. You will now be prompted for a series of agreements that you must accept from your terminal. These are included below:

Here click enter

When you see the Terms of Service (TOS) use your down arrow key to get through the text

After you finish scrolling through the TOS type the word 'yes' to move on

Confirm the installation by clicking the 'return' key

Finalize the installation by typing 'yes' and clicking enter

8. Close your ubuntu window and open a new ubuntu window.

9. Check if conda is successfully installed on your computer. Paste in your ubuntu:

conda -V

10. If the conda is sucessfully installed, you will see a message similar to the one below (versions can differ). Proceed to the antiSMASH Installation section.

conda 24.5.0

🌱 antiSMASH Installation (Windows)

todo