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Installation Guide

Important

The installation instructions provided here are explicitly for bigscape version 1.1.5 and provides no guarantee of support for other versions.

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 BiG-SCAPE as long as you read this guide thoroughly.

Installation Steps

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. 🍻 Brew Installation
  2. 🐍 Miniconda Installation
  3. ⚙️ BiG-SCAPE Installation

For Windows:

  1. 🐧 WSL Installation
  2. 🐍 Miniconda Installation
  3. ⚙️ BiG-SCAPE Installation

Terminal, Powershell, and Ubuntu

For Mac based installation instructions you will exclusively be using the terminal application to interact with your computer.

For Windows based installation instructions you will be using both PowerShell and ubuntu at any given step.
To open the terminal - click the Launchpad icon in the Dock, type terminal in the search field, then click terminal.
To open the PowerShell - open the Start menu, type Windows PowerShell, select Windows PowerShell, then select Run as Administrator.
To open the ubuntu application - open the Start menu, type ubuntu, select ubuntu, then select Open.

"How To Use" This Guide

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

  • 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

  • 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:~$ |

Mac Based Installation

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

🍻 Brew Installation (Mac)

  1. Check if brew is already installed on your computer. Open your terminal application (Finder > Application > Terminal) and paste into your terminal:
brew -v
  1. If brew is already installed, you will see a message similar to the one below (versions can differ). Proceed to the Miniconda Installation section.
Homebrew 4.3.7
  1. If you see the message below - proceed to step 4:
zsh: command not found: brew
  1. ⌛ Copy and paste the following command into your terminal and click return:
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

between 4 and 5 you have to add press enter

  1. When prompted for your password as seen below, type your computer login password.

Note

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

  1. ⌛ The installation will ask you to click return to continue:

  1. Paste into your terminal - replace bigscape with your username - the command is explicitly printed by the brew installation during the mention of next steps:

 (echo; echo 'eval "$(/opt/homebrew/bin/brew shellenv)"') >> /Users/$USERNAME/.zprofile
  1. Paste into your terminal:
eval "$(/opt/homebrew/bin/brew shellenv)"
  1. Check if brew is successfully installed on your computer. Paste:
brew -v
  1. If brew is successfully installed, you will see a message similar to the one below (versions can differ). Proceed to the Miniconda Installation section.
Homebrew 4.3.7

🐍 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.


Accidentally clicked the wrong installer in demo, but downloaded the correct one. Use the one referenced in the guide.

  1. Check if conda is already installed on your computer. Paste in your terminal :
conda -V
  1. If the conda is already installed, you will see a message similar to the one below (versions can differ). Proceed to the BiG-SCAPE Installation section.
conda 24.5.0
  1. If the conda is not installed, then you will see the message below - proceed to step 4:
zsh: command not found: conda
  1. 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

  1. Open a new terminal window and copy-paste the command below:
cd downloads
  1. ⌛ Paste into your terminal:
bash Miniconda3-latest-MacOSX-x86_64.sh
  1. 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


Click `enter` to bring up the Terms of Service


⌛⌛⌛ 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


⌛ Continue the installation by clicking the 'return' key


Type `yes` to finish the installation

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

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

conda -V
  1. If the conda is sucessfully installed, you will see a message similar to the one below (versions can differ). Proceed to the BiG-SCAPE Installation section.
conda 24.5.0

⚙️ BiG-SCAPE Installation (Mac)

  1. Open a new terminal window.

  2. Paste into your terminal:

cd Desktop && mkdir bigscape && cd bigscape
  1. Paste into your terminal:
brew install wget
  1. ⌛ Paste into your terminal:
wget https://github.com/medema-group/BiG-SCAPE/archive/refs/tags/v1.1.5.zip
  1. Paste into your terminal:
unzip v1.1.5
  1. Paste into your terminal:
cd BiG-SCAPE-1.1.5
  1. ⌛ Paste into your terminal:
conda env create -f bigscape_dependencies.yml
  1. Finally, copy and paste the command below. You will see a change in your terminal after this completes with a (bigscape) in the beginning of your line:
conda activate bigscape

  1. Validate the installation by pasting the command below:
python bigscape.py --version
  1. ⌛ Paste into your terminal:
wget https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz && gunzip Pfam-A.hmm.gz
  1. ⌛ Paste into your terminal:
hmmpress Pfam-A.hmm
  1. You should now be able to run BiG-SCAPE, perform one last verification step and copy-paste the command below to see the options for running bigscape. _Make sure that your terminal has the (bigscape) in the beginning of your line:
python bigscape.py -h


You should see this list of commands that you can use on your bigscape query.

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 bigscape installation.

🐧 WSL Installation (Windows)

  1. Check if wsl is already installed on your computer by looking 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.

  1. ⌛ Paste into your powershell:
wsl --install --distribution Ubuntu --web-download
  1. When you see the below message restart your computer and log back in to your account:
Enter new UNIX username: _

  1. After your computer restarts, the ubuntu application should now be available, open the application to verify a successful install.

  2. 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
  1. If the conda is already installed, you will see a message similar to the one below (versions can differ). Proceed to the BiG-SCAPE Installation section.
conda 24.5.0
  1. If the conda is not installed, then you will see the message below - proceed to step 4:
conda: command not found
  1. 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

  1. Open a new ubuntu window and copy-paste the command below:
WINDOWS_USER=$(/mnt/c/Windows/System32/cmd.exe /c 'echo %USERNAME%' | sed -e 's/\r//g')
  1. Copy-paste the command below:
cd ../../mnt/c/Users/$WINDOWS_USER/Downloads
  1. ⌛ Paste into your ubuntu:
bash Miniconda3-latest-Linux-x86_64.sh
  1. You will now be prompted for a series of agreements that you must accept from your ubuntu. 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

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

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

conda -V
  1. If the conda is sucessfully installed, you will see a message similar to the one below (versions can differ). Proceed to the BiG-SCAPE Installation section.
conda 24.5.0

⚙️ BiG-SCAPE Installation (Windows)

  1. Open a new ubuntu and copy-paste the command below:
WINDOWS_USER=$(/mnt/c/Windows/System32/cmd.exe /c 'echo %USERNAME%' | sed -e 's/\r//g')
  1. Copy-paste the below command:
cd ../../mnt/c/Users/$WINDOWS_USER/Documents && mkdir bigscape && cd bigscape
  1. ⌛ Paste into your ubuntu:
wget https://github.com/medema-group/BiG-SCAPE/archive/refs/tags/v1.1.5.zip
  1. Copy-paste into your ubuntu:
sudo apt install unzip
  1. Paste the below command:
unzip v1.1.5
  1. Paste into your terminal:
cd BiG-SCAPE-1.1.5
  1. ⌛ Paste into your terminal:
conda env create -f bigscape_dependencies.yml
  1. Finally, copy and paste the command below. You will see a change in your terminal after this completes with a (bigscape) in the beginning of your line:
conda activate bigscape

  1. Validate the installation by pasting the command below:
python bigscape.py --version
  1. ⌛ Paste into your terminal:
wget https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz && gunzip Pfam-A.hmm.gz
  1. ⌛ Paste into your terminal:
hmmpress Pfam-A.hmm
  1. You should now be able to run BiG-SCAPE, perform one last verification step and copy-paste the command below to see the options for running bigscape. _Make sure that your terminal has the (bigscape) in the beginning of your line:
python bigscape.py -h


You should see this list of commands that you can use on your bigscape query.

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BiG-SCAPE Installation Instructions

github.com/medema-group/BiG-SCAPE

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installation-guides big-scape

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Readme

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