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Pin Channel Commits; Decouple from Guix

Tags

  • status: closed
  • priority: medium
  • type: enhancement
  • assigned: fredm, bonfacem, aruni
  • keywords: guix-bioinformatics, guix
  • interested: pjotrp, aruni

Description

Changes in upstream Guix often lead to deployment issues, due to breakages caused by changes in how GNU Guix does things. This interrupts our day-to-day operations, leading us to scramble to fix the breakages and make the builds sane again.

In order to avoid these breakages in the future, we'll need to actually pin the commit(s) for all the channels we depend on, to avoid surprises down the line.

Channel Dependencies

We depend on the following channels in guix-bioinformatics:

  • guix: Mainline Guix channel
  • guix-past: Channel for old packages, no longer maintained on guix mainline
  • guix-rust-past-crates: Channel for rust packages using the old packaging form
  • guix-forge: Manages building containers and whatnot. The dependence is implicit here, but it is one of the main causes of breakages

Tasks

  • [x] Pin guix channel
  • [x] Pin guix-past
  • [x] Pin guix-rust-past-crates channel
  • [x] Pin guix-forge channel
  • [ ] Move packages from (gn packages bioinformatics) to upstream (gnu packages bioinformatics)

Solution

To allow guix-bioinformatics to continue improving, while preventing random breakages, we stopped depending on guix-bioinformatics directly, rather, we changed our main channel to gn-machines, and there, we pinned the version of guix-bioinformatics we depend on.

This allows us to continue updating our packages while keeping the channel dependencies relatively stable.

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