laceysanderson

laceysanderson

$view_name = 'tripal_feature_user_feature';
$query = array(
  'uniquename' => '',
  'name' => '',
  'organism' => 'All',
  'type_id' => 677,
);

// First programmatically pull up the view object.
$view = views_get_view($view_name);

laceysanderson

<?php
/**
 * @script
 * Compare functions between two github repositories to ensure backwards compatibility.
 * This script will work despite functions being reorganized into different files/order.
 */

// include the Diff class to compare our functions.
// This class can be obtained at http://code.stephenmorley.org/php/diff-implementation/
// with all rights and many thanks going to Stephen Morley.

laceysanderson

A script to generate a large SNP dataset and save it directly into chado.

REQUIRES your Drupal database user to be a PostgreSQL Superuser.

This script is compatible with the ND Genotype module (2.x) method of storing genotypes in the genotype_call table. It has been designed with efficiency in mind and thus uses COPY rather than individual inserts. Furthermore, copies are done in chunks (size can be set) in order to keep file sizes in check.

Data Storage Model: https://github.com/UofS-Pulse-Binfo/nd_genotypes/wiki/How-to-Store-your-Data#method-2-custom-genotype-call-table

laceysanderson

---
# `vagrant_box` can also be set to geerlingguy/centos6, geerlingguy/centos7,
# geerlingguy/ubuntu1404, geerlingguy/ubuntu1204, parallels/ubuntu-14.04, etc.
vagrant_box: geerlingguy/ubuntu1604
vagrant_user: vagrant
vagrant_synced_folder_default_type: nfs

# If you need to run multiple instances of Drupal VM, set a unique hostname,
# machine name, and IP address for each instance.
vagrant_hostname: drupalvm.dev

laceysanderson

#!/user/bin/perl -w
use strict;
use warnings;

# Purpose: Prefix all records names in a FASTA file.
# Arguements:
# 1. Input FASTA file
# 2. Output FASTA File
# 3. Prefix that you would like added to all the FASTA records.

laceysanderson

<?php
#!/usr/bin/env drush
/**
 * Tests 3 queries on the current Drupal/Tripal site and reports the results.
 *
 * ALL OPTIONS ARE REQUIRED.
 * SCRIPT TAKES 4hrs to RUN.
 *
 * @option --germplasm
 *   A comma-seperated list of germplasm_ids to use in the queries.

laceysanderson

<?php
#!/usr/bin/env drush
/**
 * Tests 3 queries on the current Drupal/Tripal site and reports the results.
 *
 * ALL OPTIONS ARE REQUIRED.
 * SCRIPT TAKES 4hrs to RUN.
 *
 * @option --trait_id
 *   The primary key for the trait to test.

laceysanderson

1. Check Repository for:

• License (BRONZE)
• Public Release (BRONZE)
• Latest releases should follow 7.x-version format (SILVER)
• an includes/TripalFields directory (SILVER)
• an includes/TripalImporter directory (GOLD)
• a tests directory (GOLD)

2. Check the README/docs for:

• Installation Instructions (BRONZE)
• Admin/Usage Instructions (BRONZE)

laceysanderson

This GIST provides a template for PRs requesting Tripal Extension Module Badges. Add Yes, No (with couple word explanation) or Not appicable (with couple word explanation) under status for each requirement. Making the status a link to an example of how this requirement is fullfilled is recommended but not required.

This module rating system is meant to aid Tripal Site Administrators in choosing extension modules for their site. It is also meant to guide developers in module best practices and celebrate modules which achieve these goals.

We encourage Tripal module developers to rate their modules. This can be done by Adding your Module to this list!