Bradford Condon PhD

Bioinformatics, Web & Mobile Development


drupal

This week, we’ll be moving the Tripal documentation over to ReadTheDocs. I’ve already put the Tripal DevSeed documentation online.

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This post will talk about the reasons for this decision, and a quick “how to” guide.

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This guide is for developers looking to contribute code to the core Tripal project. It introduces the testing philosophy and guidelines for Tripal core. Tripal uses Tripal Test Suite, which brings bootstraps your Tripal site for PHPUnit. It also provides conveniences like namespacing, seeders, transactions, and data factories.

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Tripal Test Suite

For a basic introduction of Tripal Testing, please see the Test Suite repo.

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I was recently tasked with using the Tripal GFF loader to add genomic coordinates to our mRNA features. The Tripal.info tutorial covers using the GFF loader to load in features, but at Hardwoods we don’t typically follow this paradigm, and only load in features using the FASTA loader.

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Welcome to Tripal Country!

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Today I’m sharing my suggestions on how to set up your module.

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Welcome to Tripal Country!

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This week I’m excited to announce we’ve set up Travis Continuous Integration with Tripal! This means every time code is committed, we test three things:

  • Upgrade a Tripal 2 site to Tripal 3
  • Install Tripal 3 on a clean site
  • Run PHPUnit tests
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Welcome to Tripal Country!

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Tripal feature annotations might be a little unintuitive, especially for non-biologists. This guide is to solidify my own knowledge of what goes where and why: hopefully it will be helpful to some developers as well.

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Welcome to Tripal Country!

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This is a short guide to demonstrate how to create new bundle types with Chado storage in Tripal 3. It was originally written as instructions for my Tripal Alchemist module. There is a similar guide on tripal.info which you can also review.

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The 2018 Tripal hackathon took place at the Plant & Animal Genomes conference in San Diego January 11th & 12th. I’d post the itinerary and workshop sessions were, but I didn’t take great notes. Instead, I’ll share about the sessions I took part in. Thursday we discussed Controlled Vocabularies in the morning, and Tripal Core issues (generally Tripal 3 issues) in the afternoon. Friday was a general round-table and a Tripal 3 bundles and fields live demo.

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As a Tripal developer, one of the fun things I get to do is contribute not only to the Tripal project, but also other parts of GMOD, the Generic Model Organism Database Project. I attended the January 10th 2018 GMOD hackathon at the Plant and Animal Genome XXVI conference hoping to make a few small changes to Chado, the SQL database schema that HardwoodGenomics uses with Tripal.

GMOD CHADO

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