_config.yml

# This is the default format. 
# For more see: http://jekyllrb.com/docs/permalinks/
# permalink: /:categories/:year/:month/:day/:title 
permalink: /:categories/:title 

exclude: [".rvmrc", ".rbenv-version", "README.md", "Rakefile", "changelog.md", ".sublime-project", ".sublime-workspace"]
highlighter: rouge

markdown: kramdown
repository: getzlab/getzlab.github.io

# Themes are encouraged to use these universal variables 
# so be sure to set them if your theme uses them.
#
title : Getz Lab
tagline: Understand cancer cell evolution and response to therapy in terms of genomics and epigenomics
inst_broad:
  url: http://www.broadinstitute.org
  name: Broad
dept_broad_cancer_program:
  url: https://www.broadinstitute.org/cancer
  name: Cancer Program
broad_lab:
  url: https://www.broadinstitute.org/labs/getz
  name: Getz Lab @ Broad
inst_mgh:
  url: https://www.massgeneral.org
  name: MGH
dept_mgh_pathology:
  url: https://www.massgeneral.org/pathology/
  name: Department of Pathology
dept_mgh_cancer_center:
  url: https://www.massgeneral.org/cancer-center/
  name: Mass General Cancer Center
inst_hms:
  url: https://hms.harvard.edu/
  name: HMS
dept_hms_pathology:
  url: https://hms.harvard.edu/departments/pathology
  name: Department of Pathology
author :
  name : Gad Getz
  email : gadgetz@broadinstitute.org
  github : 
  twitter : 
#  feedburner : feedname

# The production_url is only used when full-domain names are needed
# such as sitemap.txt 
# Most places will/should use BASE_PATH to make the urls
#
# If you have set a CNAME (pages.github.com) set your custom domain here.
# Else if you are pushing to username.github.io, replace with your username.
# Finally if you are pushing to a GitHub project page, include the project name at the end.
#
production_url : http://getzlab.org

# All Jekyll-Bootstrap specific configurations are namespaced into this hash
#
JB :
  version : 0.3.0

  # All links will be namespaced by BASE_PATH if defined.
  # Links in your website should always be prefixed with {{BASE_PATH}}
  # however this value will be dynamically changed depending on your deployment situation.
  #
  # CNAME (http://yourcustomdomain.com)
  #   DO NOT SET BASE_PATH 
  #   (urls will be prefixed with "/" and work relatively)
  #
  # GitHub Pages (http://username.github.io)
  #   DO NOT SET BASE_PATH 
  #   (urls will be prefixed with "/" and work relatively)
  #
  # GitHub Project Pages (http://username.github.io/project-name)
  #
  #   A GitHub Project site exists in the `gh-pages` branch of one of your repositories.
  #  REQUIRED! Set BASE_PATH to: http://username.github.io/project-name
  #
  # CAUTION:
  #   - When in Localhost, your site will run from root "/" regardless of BASE_PATH
  #   - Only the following values are falsy: ["", null, false]
  #   - When setting BASE_PATH it must be a valid url.
  #     This means always setting the protocol (http|https) or prefixing with "/"
  BASE_PATH : false

  # By default, the asset_path is automatically defined relative to BASE_PATH plus the enabled theme.
  # ex: [BASE_PATH]/assets/themes/[THEME-NAME]
  #
  # Override this by defining an absolute path to assets here.
  # ex: 
  #   http://s3.amazonaws.com/yoursite/themes/watermelon
  #   /assets
  #
  ASSET_PATH : false

  # These paths are to the main pages Jekyll-Bootstrap ships with.
  # Some JB helpers refer to these paths; change them here if needed.
  #
  archive_path: /archive.html
  categories_path : /categories.html
  tags_path : /tags.html
  atom_path : /atom.xml
  rss_path : /rss.xml

  # Settings for comments helper
  # Set 'provider' to the comment provider you want to use.
  # Set 'provider' to false to turn commenting off globally.
  #
  comments :
    provider : false
    disqus :
      short_name : jekyllbootstrap
    livefyre :
      site_id : 123
    intensedebate :
      account : 123abc
    facebook :
      appid : 123
      num_posts: 5
      width: 580
      colorscheme: light
   
  # Settings for analytics helper
  # Set 'provider' to the analytics provider you want to use.
  # Set 'provider' to false to turn analytics off globally.
  #
  analytics :
    provider : "google-gtag"
    google : 
      measurement_id : "G-0KJ9JWWQJV"

  # Settings for sharing 
  # Sharing is for things like tweet, plusone, hn upvotes, like, linkedin
  # Add a tweet button    => provider : tweet
  # Add a like button     => provider : like (you also need a facebook appid)
  # Add a plus one button   => provider : plusone
  # Add a HN button     => provider : hn
  # Add them all (i.e. hn + tweet + plusone + like) => provider : all
  # Set 'provider' to the sharing provider you want to use.
  # Set 'provider' to false to turn sharing off globally.
  #
  sharing :
   provider : tweet
   twitter :
     size :
     via :
     count :
   facebook :
     appid : 123
     layout : button_count
     font :
     faces : false
     width : 90
   googleplus :
     size : medium
     width :
     annotation : bubble
   linkedin :
     counter : right      
    
  # Settings for all other include helpers can be defined by creating 
  # a hash with key named for the given helper. ex:
  #
  #   pages_list :
  #     provider : "custom"   
  #
  # Setting any helper's provider to 'custom' will bypass the helper code
  # and include your custom code. Your custom file must be defined at:
  #   ./_includes/custom/[HELPER]
  # where [HELPER] is the name of the helper you are overriding.
  
# allow page redirection
plugins_dir:
  - jekyll-redirect-from
  
plugins:
  - jekyll-twitter-plugin
  - jekyll-seo-tag
  - jekyll-sitemap

current_tools:
  - name: DeTiN
    repo: getzlab/deTiN
  - name: MutSig2CV
    repo:  getzlab/MutSig2CV
  - name: CLUMPS 2
    repo: getzlab/CLUMPS2
  - name: RNA-SeQC 2
    repo: getzlab/rnaseqc
  - name: SignatureAnalyzer
    repo: getzlab/SignatureAnalyzer
  - name: MuTect 1
    repo: getzlab/mutect
  - name: MSMuTect 2
    repo: getzlab/MSMuTect2
  - name: ABSOLUTE
    repo: getzlab/ABSOLUTE
  - name: GISTIC 2
    repo: broadinstitute/gistic2
  - name: MSMutSig
    repo: getzlab/MSMutSig
  - name: PhylogicNDT
    repo: broadinstitute/PhylogicNDT
  - name: PHIAL
    repo: vanallenlab/phial
  - name: tensorQTL
    repo: broadinstitute/tensorqtl
  - name: AsymTools 2
    repo: getzlab/AsymTools2

retired_tools:
  - name: CLUMPS
    repo: getzlab/CLUMPS
  - name: MSMuTect1
    repo: getzlab/MSMuTect1