Updating Janis

Janis may seem like (an organised) chaos of individual Python packages, but they’re individual to ensure proper separation of concerns, and allows us to provide bug fixes to each section separately.

The primary Janis module janis-pipelines (RELEASES page) contains a list of all the packages and their versions. But sometimes we make quick bug fixes to individual projects, without doing a big release of the whole project.

We recommend sticking to these major releases, you can update Janis to the latest major release with:

pip3 install --no-cache --upgrade janis-pipelines

Power users

Okay, so you’re a power user and like to live on the edge. You need to decide now whether you like to live close to the cliff, or on the bleeding edge:

  • Close-ish: Installing specific modules from Pip
  • Bleeding edge: Installing individual projects from GitHub.

Installing from Pip

Janis projects follow a predictable naming structure:

With one except, janis-assistant is called janis-pipelines.runner for legacy reasons.

You could for example update janis-core with:

pip3 install --no-cache --upgrade janis-pipelines.core

Bleeding edge: From GitHub

You should be warned that builds from GitHub are not always stable, and sometimes projects get released together as they contain inter-dependencies. We’d also recommend that you install from GitHub with the --no-dependencies flag.

Due diligence over, you can install from GitHub with the following line (replacing the GitHub link with the GitHub repo you’re trying to install).

pip3 install --no-cache --upgrade --no-dependencies git+https://github.com/PMCC-BioinformaticsCore/janis-<project>.git