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bioSyntax Installation

version 0.1-beta Visit http://bioSyntax.org/install for webpage version of this file.

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

{: .language-bash}

Note: Some of the installation script requires sudo/admin privileges 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.

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.
  • 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.
  • Pick the right file type from the drop-down menu at the bottom-right corner of the editor (e.g. fasta) and select the bioSyntax Color Scheme from Preferences > Color Scheme > 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/

    {: .language-bash}

  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>

    {: .language-bash}

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

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

    {: .language-bash}

  2. 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). Select the bioSyntax Color Scheme from the Preferences menu.

  3. Restart Sublime and you now have pretty formats!

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

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>

    {: .language-bash}

  1. 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>

    {: .language-bash}

  1. Restart gedit and select the bioSyntax theme

    Edit > Preferences > Font & Color > bioSyntax

  2. 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

{: .langauge-bash}

Manual instructions (may require sudo/admin privileges)

  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

    {: .language-bash}

  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

    {: .language-bash}

  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/

    {: .language-bash}

  5. Restart vim and you now have pretty formats! NOTE: Syntax-highlighting can be turned off using :syntax off or removing the :syntax enable line from the .vimrc/_vimrc file.

less (Hardest installation, sudo privileges may be required)

(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 https://raw.githubusercontent.com/Homebrew/install/master/install)"
 else
 	brew update
 fi

    {: .language-bash}

  1. 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
 else
 	brew install source-highlight
 fi

    {: .language-bash}

  1. Unzip the downloaded bioSyntax release, $bioSyntax.

  2. 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>

    {: .language-bash}

  1. Copy the bioSyntax language definition *.lang and style definition *.style files to the paths as above:

    cp $bioSyntax/less/*.style <insert-path>
cp $bioSyntax/less/*.lang <insert-path>

    {: .language-bash}

  2. Find where source-highlight installed its src-hilite-lesspipe.sh script, and replace it with $bioSyntax/less/src-hilite-lesspipe-bio-<OS>.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

    {: .language-bash}

  3. 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
 #         ...

    {: .language-bash}

     cat $bioSyntax/less/rc_append.txt >> $RCFILE

    {: .language-bash}

  • 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

 # ...

    {: .language-bash}

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

Uninstalling bioSyntax