tripal_phylotree

A tripal module for Chado phylogeny schema, developed for LIS http://legumeinfo.org.

An example gene family: http://legumeinfo.org/chado_phylotree/phytozome_10_2.59027077

The Tripal Phylogeny module, http://tripal.info/extensions/modules/phylogeny , was initially based on this code. Tripal Phylogeny is more generic, and supports taxonomy trees as well. This LIS phylotree module is more oriented towards client side javascript features, for example using the BioJS MSA viewer.

Server Requirements

• Tripal 2 http://tripal.info/
• Chado http://gmod.org/wiki/Chado_Phylogeny_Module
• Drupal 7 https://www.drupal.org/

Server Quickstart

• git clone repository into drupal/sites/all/modules/tripal
• drush pm-enable tripal_phylotree (or enable via drupal ui admin interface)
• see in browser admin/modules, and enable tripal_phylotree permissions: add 'View Phylotree' permission to all Roles add 'Administer Phylotree' permission to Admin role(s)
• see in browser admin/tripal/extension/tripal_phylotree, go to Sync tab
• sync phylotrees
• sync organisms
• sync features of type = 'polypeptide'
• browse to /chado_phylotree/{family}, e.g. /chado_phylotree/phytozome_10_2.59026827

Javascript Build Steps

The coordinated UI views of the phylogram, the taxa pie chart, and the msa visualization are implemented using several javascript libraries. To build and bundle the javascript application you will need:

• Node 4 or newer
• Npm 3 or newer
• Git

# install aurelia-cli so the au command is on your path
npm install aurelia-cli -g

# install the javascript dependencies from the package.json manifest
cd theme/js/aurelia/
npm install

# build for development
au run --watch

# build for production (produces minified javascript)
au build --env prod

warning: on freebsd, you may have to repeat the npm install 2-3 times until all the packages are in place.