A proof of concept of a RNA-Seq pipeline. Here we combine three technologies to handle each of the following:
- Reproducibility of software is handled by container technology
- Discoverability and Transparency are handled by installing our software in the container via a Scientific Filesystem[cite]. SCIF also lets us install the same dependencies across container technologies.
- Testing is handled by continuous integration, which understands how to interact with a scientific filesystem.
Each of these components plays a slightly different and equally important role. Without SCIF, we could have the same container with commands to execute known software inside, but the container would largely remain a black box with software mixed amongst the base operating system. Without container technologies, you could install software on your host, but (as we all know) this would likely not be a portable solution. Without testing, we couldn't be sure that our software works as we intended, and is ready to plug into some pipeline tool. Check out the documentation to get started to clone the template, write your container recipe, and then build --> test --> deploy!
If you have any questions or issues, please don't hesitate to reach out.