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.

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 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

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

Manual Install

  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!

gedit

(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!

vim

(Linux / Mac / Win)

via Pathogen

If you have Pathogen 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
    
  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!

less

(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.)
     # 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: ~/.local/share/source-highlight/ or /usr/share/source-highlight/ (requires sudo)
    • Mac: /usr/local/opt/source-highlight/share/source-highlight/
     # Linux
     cp $bioSyntax/less/biosyntax.outlang     ~/.local/share/source-highlight/
     cp $bioSyntax/less/biosyntax-vcf.outlang ~/.local/share/source-highlight/
    
     # Mac
     sudo cp $bioSyntax/less/biosyntax.outlang     /usr/local/opt/source-highlight/share/source-highlight/
     sudo cp $bioSyntax/less/biosyntax-vcf.outlang /usr/local/opt/source-highlight/share/source-highlight/
    
  5. Copy the bioSyntax language and style definition files (*.lang and *.style) to same paths as above:

     # Linux
     cp $bioSyntax/less/*.style ~/.local/share/source-highlight/
     cp $bioSyntax/less/*.lang  ~/.local/share/source-highlight/
    
     #Mac
     sudo cp $bioSyntax/less/*.style /usr/local/opt/source-highlight/share/source-highlight/
     sudo cp $bioSyntax/less/*.lang  /usr/local/opt/source-highlight/share/source-highlight/
    
  6. Find and replace source-highlight’s src-hilite-lesspipe.sh script with $bioSyntax/less/src-hilite-lesspipe_bio.sh. Make the script executable.

     # Linux (Ubuntu)
     cp $bioSyntax/less/src-hilite-lesspipe-bio.sh \
     ~/.local/share/source-highlight/
    
     sudo chmod 755 ~/.local/share/source-highlight/src-hilite-lesspipe-bio.sh
    
    
     # Mac
     sudo cp $bioSyntax/less/src-hilite-lesspipe-bio.sh \
     /usr/local/opt/source-highlight/share/source-highlight/src-hilite-lesspipe.sh
    
     sudo chmod 755 /usr/local/opt/source-highlight/share/source-highlight/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 :’(