Installing bioSyntax

bioSyntax Installation

Download bioSyntax

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

bash bioSyntax_INSTALL.sh <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. For Windows, the script runs best with the Git Bash terminal, which may be required to be run as an administrator.

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 --recurse-submodules https://github.com/bioSyntax/bioSyntax.git

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

Manual Installation

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

Sublime

(Linux / Mac / Win)

via Package Control (Easiest, no admin/sudo privileges required):

  • Install Package Control for Sublime.
  • In Sublime, Preferences > Package Control > Package Control: Install Package and search for bioSyntax.

Manual Install (sudo/admin privileges may be required):

  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/bioSyntax/
    • Windows: ~/AppData/Roaming/Sublime\ Text\ 3/Packages/bioSyntax/
    • Mac: ~/Library/Application\ Support/Sublime\ Text\ 3/Packages/bioSyntax/
     cp $bioSyntax/sublime/*.sublime-syntax -d <insert-path>
    
  4. Copy over the $bioSyntax/sublime/bioSyntax.tmTheme theme file

     cp $bioSyntax/sublime/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!

gedit (sudo/admin privileges may be required):

(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: $HOME/.local/share/gtksourceview-3.0/styles
    • Windows: /c/Program\ Files/gedit/share/gtksourceview-3.0/styles/
     cp $bioSyntax/gedit/bioSyntax.xml <insert-path>
    
  4. Copy the gedit *.lang files to the appropriate gtksourceview language-spec folder.
    • Linux: $HOME/.local/share/gtksourceview-3.0/language-specs
    • Windows: /c/Program\ Files/gedit/share/gtksourceview-3.0/language-specs/
     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!

vim

(Linux / Mac / Win)

via Pathogen (Easiest installation, may require sudo/admin privileges):

If you have Pathogen and Git installed:

cd ~/.vim/bundle &&
git clone https://github.com/bioSyntax/bioSyntax-vim.git

Manual install

  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
    	
     # Windows
     mkdir -p $HOME/vimfiles $HOME/vimfiles/syntax $HOME/vimfiles/ftdetect $HOME/vimfiles/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
    	
     # Windows
     touch $HOME/_vimrc
     if ! grep -q ":syntax enable" $HOME/_vimrc; then echo ":syntax enable\\n" >> $HOME/_vimrc; fi
    
  4. Copy the vim syntax, auto-detection, and colour files from bioSyntax/vim into the respective vim folders:

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

less (Hardest installation, sudo privileges may be required)

(Linux, Mac) NOTE: Syntax-highlighting can be turned off using :syntax off or removing the :syntax enable line from the .vimrc/_vimrc file.

  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.)
     # Mac
     which -s brew
     if [[ $? != 0 ]] ; then
         ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
     else
         brew update
     fi
    
  2. Install source-highlight to your system:
    • Linux: sudo apt-get install source-highlight
    • Mac: (install/update via brew)
     # Mac
     if [[ ! -z `brew ls --versions "source-highlight"` ]]; then
         brew upgrade source-highlight
     else
         brew install source-highlight
     fi
    
  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: $HOME/.local/share/source-highlight
    • Mac: /usr/local/opt/source-highlight/share/source-highlight/
     cp $bioSyntax/less/bioSyntax.outlang <insert-path>
     cp $bioSyntax/less/bioSyntax-vcf.outlang <insert-path>
    
  5. Copy the bioSyntax language and style definition files (*.lang and *.style) to same paths as above:

     cp $bioSyntax/less/*.style <insert-path>
     cp $bioSyntax/less/*.lang <insert-path>
    
  6. Find and replace source-highlight’s src-hilite-lesspipe.sh script with $bioSyntax/less/src-hilite-lesspipe_bio.sh. Make the script executable.

     # Ubuntu
     cp $bioSyntax/less/src-hilite-lesspipe-bio-LINUX.sh \
     $HOME/.local/share/source-highlight/src-hilite-lesspipe-bio.sh
    
     chmod 755 $HOME/.local/share/source-highlight/src-hilite-lesspipe-bio.sh
    	
     # Mac
     cp $bioSyntax/less/src-hilite-lesspipe-bio-MAC.sh \
     /usr/local/bin/src-hilite-lesspipe.sh
    	
     chmod 755 /usr/local/bin/src-hilite-lesspipe.sh
    
  7. In the $bioSyntax/less/ folder, append the appropriate *_append.txt file to your shell configuration file (rc file).
    • Linux: Use $bioSyntax/less/rc_append.txt
     # Check your shell
     echo $SHELL
     # Outputs:
     '          $SHELL            $RCFILE '
     #         /bin/zsh    -->   ~/.zshrc
     #         /bin/sh     -->   ~/.shrc
     #         /bin/bash   -->   ~/.bashrc
     #         ...
    
     cat $bioSyntax/less/rc_append.txt >> ~/.zshrc
    
  • 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;
          fi
      fi
    
  1. Restart your computer for your rc files to update, open a file with less and you now have pretty formats!

Uninstalling bioSyntax :’(