bioSyntax Installation

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

Sublime
gedit
vim
less
vscode

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):

Install Sublime Text 3.

Unzip the downloaded bioSyntax release.

 unzip bioSyntax-<release>.zip -d ./bioSyntax/

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>
```

Copy over the $bioSyntax/sublime/bioSyntax.tmTheme theme file

 cp $bioSyntax/sublime/bioSyntax.tmTheme -d <insert-path>

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)
Restart Sublime and you now have pretty formats!

gedit

(Linux / Win)

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

Install Gedit.
Unzip the downloaded bioSyntax release.
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>
```
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>
```
Restart gedit and select the bioSyntax theme

Edit > Preferences > Font & Color > bioSyntax
You now have pretty formats!

via Debian/Ubuntu repositories:

bioSyntax-gedit will be available into official repositories of Debian 10 and Ubuntu 18.10 (both are not yet released).

Meanwhile, you can manually install deb package available here or using the bioSyntax PPA:

```
sudo add-apt-repository ppa:biosyntax/ppa
sudo apt-get update
sudo apt-get install biosyntax-gedit
```

Once, the package is installed, please read /usr/share/doc/biosyntax-gedit/README.Debian to activate the plugin.

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

Unzip the downloaded bioSyntax release.

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

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

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/

Restart vim and you now have pretty formats!

via Debian/Ubuntu repositories:

bioSyntax-vim will be available into official repositories of Debian 10 and Ubuntu 18.10 (both are not yet released).

Meanwhile, you can manually install deb package available here or using the bioSyntax PPA:

```
sudo add-apt-repository ppa:biosyntax/ppa
sudo apt-get update
sudo apt-get install biosyntax-vim
```

Once, the package is installed, please read /usr/share/doc/biosyntax-vim/README.Debian to activate the plugin.

less

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

Manual Install (Hardest installation, sudo privileges may be required):

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
```

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

Unzip the downloaded bioSyntax release, $bioSyntax.
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>
```
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>
```

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

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

Restart your computer for your rc files to update, open a file with less and you now have pretty formats!

via Debian/Ubuntu repositories:

bioSyntax-less will be available into official repositories of Debian 10 and Ubuntu 18.10 (both are not yet released).

Meanwhile, you can manually install deb package available here or using the bioSyntax PPA:

```
sudo add-apt-repository ppa:biosyntax/ppa
sudo apt-get update
sudo apt-get install biosyntax-less
```

Once, the package is installed, please read /usr/share/doc/biosyntax-less/README.Debian to activate the plugin.

vscode

(Linux / Mac / Win)

Caution: Installing bioSyntax will change your "User Theme" colors in VScode for all file-formats, not just bio file formats.

Open Visual Studio Code
Open Extensions (Ctrl+Shift+X for Windows/Linux and ⇧+⌘+X for Mac)
Search “bioSyntax”
Click Install
When you open a bioSyntax-compatible file, the theme should automatically be applied. However, if it doesn’t change, you can manually change your theme to bioSyntax (Ctrl+K Ctrl+T for Windows/Linux and ⌘+K ⌘+T for Mac).

bioSyntax Installation

Forking bioSyntax for development

Manual Installation

Sublime

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

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

gedit

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

via Debian/Ubuntu repositories:

vim

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

Manual install

via Debian/Ubuntu repositories:

less

Manual Install (Hardest installation, sudo privileges may be required):

via Debian/Ubuntu repositories:

vscode

Uninstalling bioSyntax :’(