Written by: C. Titus Brown
Primary Source: Living in an Ivory Basement
The khmer team is pleased to announce the release of khmer version 1.0. khmer is our software for working efficiently with fixed length DNA words, or k-mers, for research and work in computational biology.
khmer v1.0 is the culmination of about 9 months of development work by Michael Crusoe (@biocrusoe). Michael is the software engineer I hired on our NIH BIG DATA grant, and he’s spent at least half his time since being hired wrangling the project into submission.
What is new?
The last nine months has been a process+code extravaganza. Here are some of the things we did for 1.0, with an emphasis on the parts of the process we changed:
- Added continuous integration. Thanks in part to a Rackspace VM, pull requests on github trigger builds and unit tests via Jenkins!
- Moved to a pull request model for development.
- Instituted code reviews and a development checklist.
- Made khmer pip-installable.
- Moved to a unified cross-platform build system.
- Normalized our command line arguments and made the CLI documentation be auto-generated from the code.
- Moved to semantic versioning.
- Built a Galaxy interface.
- Added code coverage analysis of both C++ and Python code to our continuous integration system.
- Introduced a CITATION file and modified the scripts to output citation information.
- Wrote a citation handle for the software.
- Built better user-focused documentation.
- Starting using parts of the khmer protocols for acceptance testing.
Why did we do all this work!?
The short answer is, we like it when our software works. khmer is becoming increasingly broadly used, and it would be good if the software were to continue working.
A slightly longer answer is that we are continuing to improve khmer — we’re making it faster, stronger, and better — while we’re also doing research with it. We want to make sure that the old stuff keeps working even as we add new stuff.
But it’s not just that. There are now about five people working on fixing, improving, and extending khmer — several of them are graduate students, working on kick-ass new functionality as part of their PhDs. By having testing infrastructure that better ensures the stability and reliability of our software, each graduate student can work out on their own long branch of functionality, and — when they’re ready — they can merge their functionality back into the stable core, and we can all take advantage of it.
Actually, it’s even more. We’re building an edifice here, and we need to have a stable foundation. One very important addition that just came last weekend was the addition of khmer acceptance testing — making sure that khmer not only works as we expect it to, but integrates with other tools. For this, we turned to the khmer protocols, our nascent effort to build open, integrated pipelines for certain kinds of sequence analysis.
Our acceptance testing consists of running from raw data through the assembly stage of the Eel Pond mRNAseq assembly protocol, albeit with a carefully chosen data subset. This takes less than an hour to run, but in that hour it tests some of the core functionality of khmer at the command line, on real data. We hope to extend this into the majority of our functionality over time — for now we’re mostly just testing digital normalization and read manipulation.
Having passing acceptance tests before a major release is both extraordinarily reassuring and quite useful: in fact, it caught several last minute bugs that we’d missed because of either incomplete unit and functional tests, OR because they were bugs at the integration level and not at the unit/functional level.
And one interesting side note — our acceptance tests encompass Trimmomatic, fastx, and Trinity. That’s right, we’re passively-aggressively testing other people’s software in our acceptance tests, too ;).
Better Science Through Superior Software
Ultimately, this improved infrastructure and process lets us confidently move forward with new features in khmer, lets my group work in concert on orthogonal new features, enables larger processes and pipelines with less fear, uncertainty, and doubt, and — ultimately — should result in significant time savings as extend our research program. My firm belief is that this will allow us to do better science as we move forward.
Watch This Space. We’ll let you know how it goes.
Latest posts by C. Titus Brown (see all)
- On gaining tenure as an open scientist - December 26, 2014
- My review of “Determining the quality and complexity of NGS…” - December 18, 2014
- The post-apocalyptic world of binary containers - December 17, 2014