Installing bioSyntax

bioSyntax Installation

Download bioSyntax

bioSyntax comes with a handy installation script. Simply download the latest release and run:

bash <editor-of-choice>

# <editors> = vim || less || gedit || sublime

Note: Some of the installation script requires super-user commands at the moment. If you don’t have permissions or don’t like this; simply follow the Manual Installation instructions below, but some files will need to be placed in paths accessed via root as well.

Cloning / Forking bioSyntax for development

For installing bioSyntax, download the latest zip release.

To clone/fork the complete bioSyntax repository including development files and submodules, use:

git clone --recursive

# Or if you already cloned it
git submodule update --init

Manual Installation

  1. Sublime
  2. gedit
  3. vim
  4. less


(Linux / Mac / Win)

  1. Install Sublime Text 3.

  2. Unzip the downloaded bioSyntax release.

     unzip bioSyntax-<release>.zip -d ./bioSyntax/
  3. Copy the $bioSyntax/sublime/*.sublime-syntax files into the Sublime Packages folder:
    • Linux: ~/.config/sublime-text-3/Packages/User/
    • Windows: ~/AppData/Roaming/Sublime\ Text\ 3/Packages/User/
    • Mac: /Library/Application\ Support/Sublime\ Text\ 3/Packages/User/
     cp $bioSyntax/*.sublime-syntax -d <insert-path>
  4. Copy over the $bioSyntax/sublime/*.sublime-settings settings and $bioSyntax/sublime/bioSyntax.tmTheme theme files

     cp $bioSyntax/*.sublime-settings -d <insert-path>
     cp $bioSyntax/bioSyntax.tmTheme -d <insert-path>
  5. Formats should auto-detect; you can select a specific syntax at the drop-menu at the bottom-right corner of the window (e.g. Plain Text)

  6. Restart Sublime and you now have pretty formats!

We’re working on adding bioSyntax intallation via Sublime’s Package Control. (NOT IMPLEMENTED YET)

  • Install Package Control for Sublime.
  • Once installed, in Sublime, go to Preferences > Package Control > Package Control: Install Package and search for bioSyntax, and click on it. Package Control will install the syntax files for you.


(Linux / Win)

  1. Install Gedit.
  2. Unzip the downloaded bioSyntax release.
  3. In bioSyntax folder copy gedit style, $bioSyntax/gedit/bioSyntax.xml, file to the appropriate gtksourceview styles folder.
    • Linux: /usr/share/gtksourceview-3.0/styles/
    • Windows: /c/Program\ Files/gedit/share/gtksourceview-3.0/styles/
     sudo cp $bioSyntax/gedit/bioSyntax.xml <insert-path>
  4. Copy the gedit *.lang files to the appropriate gtksourceview language-spec folder.
    • Linux: /usr/share/gtksourceview-3.0/language-specs/
    • Windows: /c/Program\ Files/gedit/share/gtksourceview-3.0/language-specs/
     sudo cp $bioSyntax/gedit/*.lang <insert-path>
  5. Restart gedit and select the bioSyntax theme

    Edit > Preferences > Font & Color > bioSyntax'

  6. You now have pretty formats!


(Linux / Mac / Win)

via Pathogen

If you have Pathogen installed:

cd ~/.vim/bundle &&
git clone

Manual instructions

  1. Unzip the downloaded bioSyntax release.
  2. Find your vim profile folder, and make a syntax, ftdetect, and colors directories in it, if they don’t exist.
    • Linux/Mac: ~/.vim/
    • Windows: $HOME/vimfiles/
     # Linux/Mac
     mkdir -p ~/.vim ~/.vim/syntax ~/.vim/ftdetect ~/.vim/colors
  3. Turn on syntax highlighting by default in your vim configuration file. (~/.vimrc or $HOME/_vimrc)

     # Linux/Mac
     touch ~/.vimrc
     if ! grep -q "syntax enable" ~/.vimrc; then echo "syntax enable\\n" >> ~/.vimrc; fi
  4. Copy the vim syntax, auto-detection, and colour files from bioSyntax/vim into the respective vim folders:

     cp $bioSyntax/vim/*.vim ~/.vim/syntax/
     cp $bioSyntax/vim/ftdetect/*.vim ~/.vim/ftdetect/
     cp $bioSyntax/vim/colors/bioSyntax.vim ~/.vim/colors/
  5. Restart vim and you now have pretty formats!


(Linux, Mac)

  1. Ensure that your applications/packages are up-to-date:
    • Linux: sudo apt-get update
    • Mac: (Installing source-highlight is easiest via homebrew. The following updates brew if it is installed; installs it otherwise.)
     which -s brew
     if [[ $? != 0 ]] ; then
         ruby -e "$(curl -fsSL"
         brew update
  2. Install source-highlight to your system:
    • Linux: sudo apt-get install source-highlight
    • Mac: (install/update via brew)
     if [[ ! -z `brew ls --versions "source-highlight"` ]]; then
         brew upgrade source-highlight
         brew install source-highlight
  3. Unzip the downloaded bioSyntax release, $bioSyntax.

  4. In the $bioSyntax/less/ folder, copy the biosyntax.outlang and biosyntax-vcf.outlang files to the source-highlight folder:
    • Linux: /usr/share/source-highlight/
    • Mac: /usr/local/opt/source-highlight/share/source-highlight/
     sudo cp $bioSyntax/less/biosyntax.outlang <insert-path>
     sudo cp $bioSyntax/less/biosyntax-vcf.outlang <insert-path>
  5. Copy the bioSyntax language definition *.lang and style definition *.style files to the paths as above:

     sudo cp $bioSyntax/less/*.style <insert-path>
     sudo cp $bioSyntax/less/*.lang <insert-path>
  6. Find where source-highlight installed its script, and replace it with $bioSyntax/less/ Make the script executable.

     # Ubuntu
     sudo cp $bioSyntax/less/ \
     sudo chmod 755 /usr/share/source-highlight/
  7. In the $bioSyntax/less/ folder, append the appropriate *_append.txt file to your shell configuration file (rc file).
    • Linux: Uses $bioSyntax/less/rc_append.txt
     echo $SHELL
     # Outputs:
     '          $SHELL            $RCFILE '
     #         /bin/zsh    -->   ~/.zshrc
     #         /bin/sh     -->   ~/.shrc
     #         /bin/bash   -->   ~/.bashrc
     #         ...
     cat $bioSyntax/less/rc_append.txt >> $RCFILE
  • Mac: Uses $bioSyntax/less/bp_append.txt

      if [ `echo $SHELL` == "/bin/bash" ]; then
          if ! grep -q "bioSyntax" ~/.bashrc; then
              cat $bioSyntax/less/bp_append.txt >> ~/.bashrc;
      # ...
  1. Restart your computer for your rc files to update, open a file with less and you now have pretty formats!

Uninstalling bioSyntax