serratus VS bioconda-recipes

The Laboratory for RNA-Based Lifeforms | University of Toronto | Full-Time | ONSITE

We're a research computational biology lab at the forefront of RNA virus and virus-like agent discovery. Our goal is to help prevent the next pandemic by building the technical infrastructure to assist global virology research and public-health responses.

Seeking a full-stack developer who is creative, passionate, and willing to learn. No biology experience neccesary, but are a plus. Key assets: Python/R, AWS/HPC, postgres, javascript. See full job posting: http://rrna.ca/id0002

See: Serratus (https://serratus.io)

Serratus (https://github.com/ababaian/serratus) is an OSS bioinformatics project created by a passionate group of volunteers. Short story is we're re-analyzing all of the world's DNA/RNA sequencing data to find new viruses that other people have missed. It works surprisingly well, but there's a ton left to do.

Rust makes distribution and maintenance near trivial. My lab develops a fairly widely-used tool, salmon, for the quantification of transcript expression from RNA-seq data. This tool is written in C++14, and has a substantial number of dependencies. The process of updating the tool (e.g. bumping dependencies) and cutting a new release is painful. To maintain widespread availability, we distribute this tool using bioconda which uses it's own CI and setup to build new releases for (in our case) Linux and MacOS. Things break all the time. For example, recently, they bumped the compiler used to build packages. This changed some default "implementation defined" behavior, causing previously functioning code to fail. We didn't find this locally, because we didn't test that specific compiler version. When we tried to release a new version, we had to go back and fix things etc. This is not just because different compilers exist, but because the C++ specification is soooo complicated and the set of undefined and implementation defined behavior is sooo broad that it's very brittle and it's easy for things to "break" via bitrot. However, the stability provided by Rust has been phenomenal so far. In our code, we only use stable Rust features, and we have benefited tremendously from the empirical guarantee that valid Rust code (except in exceptional cases like latent bugs in the language) will remain valid. While not all crates follow it religiously, there is a reasonable respect for semantic versioning. Thus, cutting a new release of one of our Rust tools is often as simple as just updating the Cargo.toml (and Cargo.lock in the case of applications), tagging a new release in GitHub, and letting the bioconda CI do it's business with the tagged artifacts. The build "scripts" are almost always trivial because the builds just work, across platforms, across CIs, etc. Now, new projects like cargo dist look like they make this process even simpler.

I contribute to Nextflow core (https://nf-co.re/) It's more of a collection of pipelines than traditional software, but there are users all around the world and a good community.

Most of the packages on bioconda (https://bioconda.github.io/) are open source. But you probably want to find a sub-field that interests you most before finding a project.

In grad school, we also had an ex-google software engineer volunteer with us one day a week. It was very impactful for many members of the lab to learn good engineering practices, and it wasn't at all like the sentiment others in this thread are expressing where engineers were "janitors".

Answering this because I believe there is no way other than looking at their "build.sh" in the recipes (e.g., in the build.sh of MOSCA, you can see the symbolic link in the 7th line will be mosca.py). One thing you can do to find the main script is also to run "find ~/anaconda3 (or miniconda3) -name *name_of_the_tool*" to find most of their scripts.

In my world (research science) we usually use anaconda, which is just a slightly higher-level wrapper around python virtual envs. But they also maintain more repositories of various modules that scientists need. e.g. https://bioconda.github.io/

Seems like there's a conda packaging on the works: https://github.com/bioconda/bioconda-recipes/pull/29660